Variant report

Variant	rs645184
Chromosome Location	chr11:74129133-74129134
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:74107664..74111808-chr11:74126117..74130270,5	MCF-7	breast:
2	chr11:74107862..74112061-chr11:74124805..74130360,12	MCF-7	breast:
3	chr11:73589529..73591299-chr11:74128037..74130112,2	MCF-7	breast:
4	chr11:74122725..74125748-chr11:74128034..74129993,3	MCF-7	breast:
5	chr11:74128652..74130303-chr11:74131969..74134744,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000264402	Chromatin interaction
ENSG00000254631	Chromatin interaction
ENSG00000165434	Chromatin interaction
ENSG00000175575	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10793084	0.95[CHB][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs10793085	0.95[CHB][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs10898988	0.95[CHB][hapmap];0.80[ASN][1000 genomes]
rs10898989	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.86[GIH][hapmap];0.87[JPT][hapmap];0.98[TSI][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11236106	0.82[ASN][1000 genomes]
rs12274367	0.82[ASN][1000 genomes]
rs12281178	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2509535	0.86[ASN][1000 genomes]
rs3132849	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3862800	0.95[CHB][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs484447	0.95[CHB][hapmap];0.82[CHD][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs515589	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs517303	0.83[ASN][1000 genomes]
rs520701	0.85[ASN][1000 genomes]
rs520837	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs537637	0.95[ASN][1000 genomes]
rs538805	0.86[ASN][1000 genomes]
rs539343	0.95[CHB][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs540279	0.82[ASN][1000 genomes]
rs544747	0.84[ASN][1000 genomes]
rs563722	0.95[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs56373920	0.82[ASN][1000 genomes]
rs591372	0.82[ASN][1000 genomes]
rs603502	0.82[ASN][1000 genomes]
rs612040	0.84[ASN][1000 genomes]
rs612700	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs615593	0.84[ASN][1000 genomes]
rs618993	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61901485	0.82[ASN][1000 genomes]
rs621109	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs621857	0.86[ASN][1000 genomes]
rs629134	0.86[ASN][1000 genomes]
rs633568	0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs638656	0.82[ASN][1000 genomes]
rs640500	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs642033	0.91[CHB][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs642500	0.86[ASN][1000 genomes]
rs658950	0.83[ASN][1000 genomes]
rs670722	0.86[ASN][1000 genomes]
rs670829	0.83[ASN][1000 genomes]
rs671946	0.83[ASN][1000 genomes]
rs684028	0.82[ASN][1000 genomes]
rs685684	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs692809	0.95[CHB][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs693884	0.95[CHB][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs694638	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7925353	0.95[CHB][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs7947671	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757451	chr11:73842609-74545888	Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	esv2759837	chr11:73842609-74557597	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
3	esv34979	chr11:73878688-74533452	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
4	esv2758277	chr11:73887567-74557597	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
5	nsv825994	chr11:73936667-74534455	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
6	nsv555443	chr11:74109166-74180489	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
7	nsv1041154	chr11:74114801-74177909	Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs645184	INTS4	cis	cerebellum	SCAN
rs645184	PGM2L1	cis	parietal	SCAN
rs645184	FAM168A	cis	cerebellum	SCAN

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:74126800-74130800	Enhancers	Fetal Thymus	thymus
2	chr11:74126800-74131000	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr11:74127000-74129400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
4	chr11:74127000-74129400	Enhancers	Primary T helper cells fromperipheralblood	blood
5	chr11:74127000-74129600	Enhancers	A549	lung
6	chr11:74127000-74129800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr11:74127000-74130000	Enhancers	Thymus	Thymus
8	chr11:74127200-74130000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr11:74127200-74130400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr11:74127200-74130400	Enhancers	HMEC	breast
11	chr11:74127200-74130800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr11:74127800-74129400	Enhancers	Primary T cells from cord blood	blood
13	chr11:74127800-74129400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
14	chr11:74127800-74130000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
15	chr11:74128000-74129200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
16	chr11:74128000-74129400	Enhancers	Primary T cells fromperipheralblood	blood
17	chr11:74128000-74129400	Enhancers	Primary hematopoietic stem cells	blood
18	chr11:74128000-74129400	Enhancers	Primary T helper naive cells from peripheral blood	blood
19	chr11:74128000-74129400	Enhancers	Aorta	Aorta
20	chr11:74128000-74129400	Enhancers	Esophagus	oesophagus
21	chr11:74128000-74129400	Enhancers	Pancreas	Pancrea
22	chr11:74128000-74129400	Enhancers	Rectal Mucosa Donor 31	rectum
23	chr11:74128000-74130400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr11:74128200-74129200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr11:74128200-74129400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr11:74128200-74130000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr11:74128400-74129400	Enhancers	Rectal Smooth Muscle	rectum
28	chr11:74128400-74129800	Enhancers	Muscle Satellite Cultured Cells	--
29	chr11:74128400-74130000	Enhancers	Primary T helper cells PMA-I stimulated	--
30	chr11:74128400-74130400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr11:74128400-74130600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr11:74128400-74130600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr11:74128400-74130600	Enhancers	Osteobl	bone
34	chr11:74128400-74131000	Enhancers	Hela-S3	cervix
35	chr11:74128400-74131000	Enhancers	NH-A	brain
36	chr11:74128600-74129200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
37	chr11:74128600-74129200	Enhancers	Duodenum Mucosa	Duodenum
38	chr11:74128600-74129200	Enhancers	Placenta Amnion	Placenta Amnion
39	chr11:74128600-74129200	Enhancers	Sigmoid Colon	Sigmoid Colon
40	chr11:74128600-74129400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
41	chr11:74128600-74129400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr11:74128600-74129400	Enhancers	Stomach Smooth Muscle	stomach
43	chr11:74128600-74129400	Enhancers	NHLF	lung
44	chr11:74128600-74130000	Enhancers	Colon Smooth Muscle	Colon
45	chr11:74128600-74130000	Enhancers	HSMM	muscle
46	chr11:74128600-74130000	Enhancers	NHDF-Ad	bronchial
47	chr11:74128600-74130600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr11:74128600-74130600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr11:74128600-74130600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr11:74128600-74130600	Enhancers	HSMMtube	muscle

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