Variant report

Variant	rs17136841
Chromosome Location	chr7:16963044-16963045
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:16962681..16964346-chr7:16965183..16967414,2	MCF-7	breast:
2	chr7:16961789..16963721-chr7:17337558..17339817,2	MCF-7	breast:
3	chr7:16961828..16963481-chr7:16965140..16966973,2	K562	blood:
4	chr7:16954984..16957560-chr7:16961614..16963759,2	MCF-7	breast:
5	chr7:16841661..16846041-chr7:16958948..16964276,7	MCF-7	breast:
6	chr7:16962023..16963912-chr7:16979161..16982109,2	K562	blood:

Variant related genes	Relation type
ENSG00000106546	Chromatin interaction
ENSG00000106541	Chromatin interaction
ENSG00000237773	Chromatin interaction

Extended variants
information (count: 85 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10228868	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10242955	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10255043	0.81[CHB][hapmap];0.90[JPT][hapmap]
rs10255179	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10258836	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10263336	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10267274	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10270184	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10275619	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.86[MEX][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10276006	0.81[CHB][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10279956	1.00[ASW][hapmap];0.81[CHB][hapmap];0.83[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1029580	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10487584	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10950640	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12113053	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs12113054	1.00[CHB][hapmap];0.94[CHD][hapmap];0.92[JPT][hapmap];0.97[ASN][1000 genomes]
rs1990114	0.92[JPT][hapmap]
rs2108091	0.83[GIH][hapmap];0.92[JPT][hapmap]
rs2389711	0.91[ASN][1000 genomes]
rs2689427	1.00[CHB][hapmap];0.83[JPT][hapmap];0.89[ASN][1000 genomes]
rs28464487	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28516514	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28525306	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28549925	0.96[ASN][1000 genomes]
rs28623255	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28711947	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4308618	0.81[CHB][hapmap];0.90[JPT][hapmap]
rs4320447	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs4368873	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs4410801	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs4534036	1.00[CHB][hapmap];0.94[CHD][hapmap];0.92[JPT][hapmap];0.97[ASN][1000 genomes]
rs55888380	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs55916518	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs56048578	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs56383312	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57241019	0.82[AFR][1000 genomes]
rs6461286	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs66954750	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs67546316	0.89[AMR][1000 genomes]
rs6952327	1.00[CHB][hapmap];0.92[JPT][hapmap];0.97[ASN][1000 genomes]
rs6952470	1.00[CHB][hapmap];0.92[JPT][hapmap];0.97[ASN][1000 genomes]
rs6968539	0.80[CHB][hapmap]
rs73069814	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs73311052	0.89[EUR][1000 genomes]
rs73313029	0.82[EUR][1000 genomes]
rs7789145	0.82[JPT][hapmap]
rs7805091	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs9691575	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs975604	0.87[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:36 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv887761	chr7:16834361-17732490	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv887762	chr7:16834361-17746628	Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv887763	chr7:16834361-17750811	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	nsv887764	chr7:16839835-17218800	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv887765	chr7:16839835-17750811	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
6	nsv1027284	chr7:16849986-17008167	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv606339	chr7:16852808-17004301	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	nsv1016695	chr7:16854300-16991627	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
9	nsv1017413	chr7:16854300-17125005	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
10	nsv538749	chr7:16854300-17125005	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
11	nsv1015831	chr7:16854300-17732227	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
12	nsv538750	chr7:16854300-17732227	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
13	nsv870171	chr7:16872876-17188633	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
14	nsv529874	chr7:16877677-17703617	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
15	nsv532093	chr7:16877677-17712291	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
16	nsv887766	chr7:16883936-16991565	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
17	nsv1034503	chr7:16900137-17033354	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
18	nsv1024829	chr7:16900137-17645026	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
19	nsv887767	chr7:16908545-16963803	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
20	nsv606340	chr7:16908545-17334899	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
21	nsv887770	chr7:16910963-16963773	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
22	nsv887771	chr7:16910963-16966355	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
23	nsv1023794	chr7:16913789-17416093	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
24	nsv606341	chr7:16915528-17405718	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
25	nsv464398	chr7:16915528-17414784	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
26	nsv606342	chr7:16915528-17414784	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
27	nsv1028248	chr7:16918221-17409752	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
28	nsv1019491	chr7:16925518-17397734	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
29	nsv887772	chr7:16932926-16989462	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
30	nsv1030274	chr7:16933440-17375962	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
31	nsv1018497	chr7:16933440-17405859	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
32	nsv1024472	chr7:16933440-17412361	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
33	nsv887773	chr7:16946486-17160612	Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Weak transcription Genic enhancers Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
34	nsv887774	chr7:16946486-17644213	Enhancers Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
35	nsv887775	chr7:16947921-17663745	Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
36	nsv949237	chr7:16959444-17635119	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17136841	CCL4	trans	brain	seeQTL
rs17136841	CCL3	trans	brain	seeQTL
rs17136841	CCL3L1	trans	brain	seeQTL

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:16957800-16966200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr7:16957800-16966200	Weak transcription	HMEC	breast
3	chr7:16958000-16966200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr7:16960200-16963400	Enhancers	Fetal Intestine Large	intestine
5	chr7:16960200-16963600	Enhancers	Fetal Intestine Small	intestine
6	chr7:16960600-16963600	Enhancers	Primary T cells from cord blood	blood
7	chr7:16961000-16973400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr7:16961400-16963600	Enhancers	Fetal Thymus	thymus
9	chr7:16961800-16963200	Enhancers	A549	lung
10	chr7:16961800-16965400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr7:16961800-16965600	Weak transcription	Hela-S3	cervix
12	chr7:16961800-16966200	Weak transcription	HepG2	liver
13	chr7:16961800-16966200	Weak transcription	HUVEC	blood vessel
14	chr7:16961800-16966200	Weak transcription	Osteobl	bone
15	chr7:16962000-16966400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr7:16962200-16963600	Enhancers	Rectal Mucosa Donor 31	rectum
17	chr7:16962600-16963200	Enhancers	Primary T helper naive cells from peripheral blood	blood
18	chr7:16962600-16963200	Enhancers	Small Intestine	intestine
19	chr7:16962600-16963600	Enhancers	Placenta Amnion	Placenta Amnion
20	chr7:16962600-16963800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr7:16962600-16966200	Weak transcription	NHEK	skin
22	chr7:16962800-16963200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
23	chr7:16962800-16963200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr7:16962800-16963600	Enhancers	Sigmoid Colon	Sigmoid Colon
25	chr7:16962800-16966200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr7:16963000-16963800	Enhancers	Stomach Mucosa	stomach
27	chr7:16963000-16965600	Weak transcription	Primary B cells from peripheral blood	blood
28	chr7:16963000-16965800	Weak transcription	Duodenum Mucosa	Duodenum
29	chr7:16963000-16966200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr7:16963000-16966200	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr7:16963000-16966200	Weak transcription	Rectal Mucosa Donor 29	rectum

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