Variant report

Variant	rs7177328
Chromosome Location	chr15:52305464-52305465
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:52262466..52265779-chr15:52303817..52307426,4	MCF-7	breast:
2	chr15:52300735..52303050-chr15:52304162..52305762,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000166477	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10152141	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10518675	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12324384	0.83[EUR][1000 genomes]
rs12324807	0.83[EUR][1000 genomes]
rs13379854	0.83[EUR][1000 genomes]
rs16964694	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs16964700	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs16964705	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs16964720	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17540338	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs17612255	0.88[ASN][1000 genomes]
rs17612326	0.81[ASN][1000 genomes]
rs2001741	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2017967	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2246726	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.91[ASN][1000 genomes]
rs2306793	1.00[EUR][1000 genomes]
rs2414120	0.88[ASN][1000 genomes]
rs2414123	0.93[ASN][1000 genomes]
rs2441779	0.91[ASN][1000 genomes]
rs2470593	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2470594	0.91[ASN][1000 genomes]
rs2470595	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2554321	1.00[GIH][hapmap]
rs2554340	0.88[ASN][1000 genomes]
rs2554341	1.00[GIH][hapmap]
rs2593189	1.00[GIH][hapmap]
rs2899484	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3099571	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4375608	0.91[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4456445	0.91[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4491448	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs4774606	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4775993	0.94[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4775995	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.87[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4775996	1.00[ASW][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4775997	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs55705935	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55714716	0.91[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs55873482	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56307802	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56677715	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs58000475	0.99[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58936667	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61546369	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs732097	0.89[CHB][hapmap]
rs7359204	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs74013636	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs74013638	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74013640	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74013641	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74013642	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74013644	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs74013645	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs74013646	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs74013647	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs74013648	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs74013653	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs74013654	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs74013656	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs74013657	0.88[ASN][1000 genomes]
rs74013659	0.81[ASN][1000 genomes]
rs74013661	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7497554	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs751560	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs8027276	0.83[EUR][1000 genomes]
rs8033365	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8033840	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs8036048	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8040728	0.82[ASN][1000 genomes]
rs8041281	0.91[ASN][1000 genomes]
rs9796534	0.91[AMR][1000 genomes];0.98[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	nsv1053788	chr15:52223389-52307138	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	nsv1047260	chr15:52257100-52337418	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
3	nsv1050664	chr15:52265723-52342101	Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
4	nsv517399	chr15:52266878-52305464	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv1536	chr15:52276293-52320919	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
6	nsv530681	chr15:52297253-52390470	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
7	nsv471244	chr15:52305463-52511465	Enhancers Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52299400-52310800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr15:52299600-52305600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr15:52299600-52310200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr15:52299600-52310600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr15:52299600-52310800	Weak transcription	HSMMtube	muscle
6	chr15:52301200-52305600	Weak transcription	Primary T cells from cord blood	blood
7	chr15:52301400-52310800	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr15:52301400-52310800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr15:52301400-52310800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr15:52301400-52310800	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr15:52301600-52305600	Enhancers	GM12878-XiMat	blood
12	chr15:52301600-52306000	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr15:52301800-52306200	Weak transcription	Primary B cells from cord blood	blood
14	chr15:52302400-52306000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr15:52302800-52306400	Enhancers	HMEC	breast
16	chr15:52303000-52305800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr15:52303600-52306200	Enhancers	A549	lung
18	chr15:52303600-52310800	Weak transcription	Pancreas	Pancrea
19	chr15:52303600-52310800	Weak transcription	Right Atrium	heart
20	chr15:52303800-52305800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr15:52303800-52306000	Enhancers	HUVEC	blood vessel
22	chr15:52303800-52306200	Enhancers	NHEK	skin
23	chr15:52303800-52306800	Enhancers	K562	blood
24	chr15:52303800-52310400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr15:52303800-52310600	Weak transcription	Osteobl	bone
26	chr15:52304200-52306400	Enhancers	Hela-S3	cervix
27	chr15:52304200-52309200	Enhancers	Primary monocytes fromperipheralblood	blood
28	chr15:52304400-52310400	Weak transcription	NHLF	lung
29	chr15:52304400-52310600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr15:52304400-52310800	Weak transcription	Fetal Muscle Leg	muscle
31	chr15:52304400-52310800	Weak transcription	Left Ventricle	heart
32	chr15:52304400-52310800	Weak transcription	Lung	lung
33	chr15:52304400-52310800	Weak transcription	Psoas Muscle	Psoas
34	chr15:52304400-52310800	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr15:52304600-52305800	Enhancers	Monocytes-CD14+_RO01746	blood
36	chr15:52304600-52310400	Weak transcription	NH-A	brain
37	chr15:52304600-52310800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr15:52304600-52310800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr15:52304600-52310800	Weak transcription	Brain Germinal Matrix	brain
40	chr15:52304600-52310800	Weak transcription	Rectal Smooth Muscle	rectum
41	chr15:52304800-52305800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr15:52304800-52310400	Weak transcription	HepG2	liver
43	chr15:52304800-52310600	Weak transcription	Adipose Nuclei	Adipose
44	chr15:52304800-52310600	Weak transcription	Brain Angular Gyrus	brain
45	chr15:52304800-52310800	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr15:52304800-52310800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr15:52304800-52310800	Weak transcription	Brain Anterior Caudate	brain
48	chr15:52304800-52310800	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr15:52304800-52310800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr15:52304800-52310800	Weak transcription	Brain Substantia Nigra	brain

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