Variant report

Variant	rs6502629
Chromosome Location	chr17:17869642-17869643
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:17868830..17871208-chr17:17873732..17875523,2	K562	blood:
2	chr17:17867285..17871471-chr17:17874516..17877381,4	MCF-7	breast:
3	chr17:17868065..17872323-chr17:17872969..17875651,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000175662	Chromatin interaction
ENSG00000171962	Chromatin interaction

Extended variants
information (count: 134 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:128)

rs_ID	r²[population]
rs10048206	0.91[CEU][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1052299	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[JPT][hapmap];0.88[MEX][hapmap]
rs11078400	0.83[CEU][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap]
rs11078404	0.82[EUR][1000 genomes]
rs11078405	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11078406	0.91[CEU][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs11078407	0.82[EUR][1000 genomes]
rs1108648	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs11650649	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.91[ASN][1000 genomes]
rs11650890	0.91[ASN][1000 genomes]
rs11652881	0.81[ASW][hapmap];0.82[JPT][hapmap]
rs11656665	0.82[JPT][hapmap]
rs11656840	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs11657074	0.91[ASN][1000 genomes]
rs11657423	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs11869536	0.82[EUR][1000 genomes]
rs11871899	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12452219	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12452254	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12600546	0.91[CEU][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12603148	0.84[EUR][1000 genomes]
rs12936037	0.91[ASN][1000 genomes]
rs12941039	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.85[TSI][hapmap];0.91[ASN][1000 genomes]
rs12943500	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12953299	1.00[CHB][hapmap]
rs16960744	0.84[MEX][hapmap]
rs1889014	0.89[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1889018	1.00[CHB][hapmap];0.83[CHD][hapmap];0.82[JPT][hapmap];0.87[MEX][hapmap]
rs2236513	0.82[JPT][hapmap]
rs2350976	0.82[JPT][hapmap]
rs2350977	0.91[CEU][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap]
rs28428991	0.82[EUR][1000 genomes]
rs28615278	0.87[YRI][hapmap]
rs2955371	0.83[CEU][hapmap];1.00[JPT][hapmap]
rs2955382	0.91[CEU][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.81[EUR][1000 genomes]
rs3183702	0.82[JPT][hapmap]
rs3744115	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[JPT][hapmap];0.88[MEX][hapmap]
rs3818717	0.82[JPT][hapmap]
rs4077198	0.82[EUR][1000 genomes]
rs4077828	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs4244602	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4257260	0.91[CEU][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4321247	0.84[AMR][1000 genomes]
rs4341796	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4343339	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4413022	0.91[CEU][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4414547	0.84[EUR][1000 genomes]
rs4459604	0.80[MEX][hapmap]
rs4470201	0.91[CEU][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs4534911	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4553680	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4616340	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4924822	0.82[JPT][hapmap];0.83[MEX][hapmap]
rs4924823	0.83[CEU][hapmap];0.84[MEX][hapmap];0.81[TSI][hapmap]
rs4925120	0.84[MEX][hapmap]
rs4925123	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.91[ASN][1000 genomes]
rs4925125	0.87[CEU][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap]
rs4925126	0.91[CEU][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap]
rs4925129	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4925130	0.91[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.81[TSI][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4925138	0.87[CEU][hapmap];0.82[JPT][hapmap];0.92[MEX][hapmap]
rs5002487	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62064156	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62064158	0.82[EUR][1000 genomes]
rs6502619	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6502622	0.91[CEU][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs6502624	0.91[CEU][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs6502625	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6502626	0.83[EUR][1000 genomes]
rs6502627	0.91[CEU][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs66531105	0.82[EUR][1000 genomes]
rs67253360	0.82[EUR][1000 genomes]
rs7207043	0.81[EUR][1000 genomes]
rs7207395	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7213225	0.91[CEU][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7214002	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs7214536	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7222480	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7224815	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7359509	1.00[CHB][hapmap];0.83[CHD][hapmap];0.82[JPT][hapmap];0.87[MEX][hapmap]
rs7501812	1.00[CHB][hapmap];0.83[CHD][hapmap];0.82[JPT][hapmap];0.87[MEX][hapmap]
rs7503334	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap];0.91[ASN][1000 genomes]
rs8065416	0.91[CEU][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes]
rs8065497	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8065563	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.91[ASN][1000 genomes]
rs8065970	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8066982	0.91[CEU][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8068820	0.82[EUR][1000 genomes]
rs8070128	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8070624	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8070722	0.82[EUR][1000 genomes]
rs8070748	0.91[CEU][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8073001	0.91[CEU][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs8075965	0.80[EUR][1000 genomes]
rs8077338	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8077530	0.80[EUR][1000 genomes]
rs8078105	0.91[CEU][hapmap];0.84[MEX][hapmap];0.80[AMR][1000 genomes]
rs8078138	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8078583	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8079321	0.83[CEU][hapmap];0.84[MEX][hapmap];0.83[TSI][hapmap]
rs8079418	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8080061	0.83[CEU][hapmap];0.84[MEX][hapmap];0.83[TSI][hapmap]
rs8080823	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs854762	0.87[CEU][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap]
rs854764	0.87[CEU][hapmap];0.82[JPT][hapmap];0.92[MEX][hapmap]
rs854765	0.87[CEU][hapmap];0.82[JPT][hapmap]
rs854766	0.87[CEU][hapmap];0.82[JPT][hapmap];0.96[MEX][hapmap]
rs854813	0.83[CEU][hapmap];0.82[JPT][hapmap];0.92[MEX][hapmap]
rs950966	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.91[ASN][1000 genomes]
rs9635697	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9635698	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9889565	0.82[YRI][hapmap]
rs9890341	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs9891957	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs9895191	0.85[YRI][hapmap]
rs9895750	0.91[ASN][1000 genomes]
rs9899634	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs9902941	0.82[JPT][hapmap];0.83[MEX][hapmap]
rs9904163	0.82[EUR][1000 genomes]
rs9905284	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9907246	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[JPT][hapmap];0.92[MEX][hapmap];0.87[TSI][hapmap];0.83[ASN][1000 genomes]
rs9907287	0.83[CEU][hapmap];0.84[MEX][hapmap];0.83[TSI][hapmap]
rs9908299	0.91[ASN][1000 genomes]
rs9908832	0.83[EUR][1000 genomes]
rs9912895	0.91[CEU][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs9913277	0.80[MEX][hapmap]
rs9913724	0.82[EUR][1000 genomes]
rs9915248	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[JPT][hapmap];0.83[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531183	chr17:17571035-18205309	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer 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	123 gene(s)	inside rSNPs	diseases
2	nsv916653	chr17:17651916-18454952	Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
3	nsv907766	chr17:17682484-17957348	Enhancers Strong transcription Flanking Active TSS Genic enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
4	nsv533142	chr17:17691726-18236686	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	116 gene(s)	inside rSNPs	diseases
5	nsv482879	chr17:17802463-17989273	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS 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	13 gene(s)	inside rSNPs	diseases
6	nsv510701	chr17:17850474-17955485	Strong transcription Active TSS Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6502629	SREBF1	cis	Whole Blood	GTEx
rs6502629	TOM1L2	cis	parietal	SCAN
rs6502629	DRG2	cis	Thyroid	GTEx
rs6502629	TOM1L2	cis	cerebellum	SCAN

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:17862200-17874000	Weak transcription	Primary hematopoietic stem cells	blood
2	chr17:17862400-17874200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr17:17863400-17874000	Weak transcription	NH-A	brain
4	chr17:17863600-17869800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr17:17863600-17873800	Weak transcription	HSMMtube	muscle
6	chr17:17863800-17869800	Weak transcription	Fetal Thymus	thymus
7	chr17:17863800-17871800	Weak transcription	Fetal Brain Male	brain
8	chr17:17863800-17872800	Weak transcription	Brain Germinal Matrix	brain
9	chr17:17863800-17873800	Weak transcription	Fetal Muscle Leg	muscle
10	chr17:17863800-17873800	Weak transcription	Thymus	Thymus
11	chr17:17863800-17874400	Weak transcription	Fetal Muscle Trunk	muscle
12	chr17:17864000-17870400	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr17:17864000-17873800	Weak transcription	HSMM	muscle
14	chr17:17864000-17874200	Weak transcription	Placenta	Placenta
15	chr17:17864000-17874400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr17:17864000-17874400	Weak transcription	Pancreas	Pancrea
17	chr17:17864200-17869800	Weak transcription	NHDF-Ad	bronchial
18	chr17:17864200-17871400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr17:17864200-17873600	Weak transcription	NHEK	skin
20	chr17:17864200-17873800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr17:17864200-17873800	Weak transcription	Duodenum Mucosa	Duodenum
22	chr17:17864200-17873800	Weak transcription	Fetal Intestine Large	intestine
23	chr17:17864200-17874000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr17:17864200-17874200	Weak transcription	Fetal Intestine Small	intestine
25	chr17:17864200-17874200	Weak transcription	Rectal Smooth Muscle	rectum
26	chr17:17864400-17872800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr17:17864400-17872800	Weak transcription	A549	lung
28	chr17:17864400-17873800	Weak transcription	Stomach Mucosa	stomach
29	chr17:17864400-17874400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr17:17864600-17872200	Weak transcription	Small Intestine	intestine
31	chr17:17864600-17873800	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr17:17864800-17869800	Weak transcription	Hela-S3	cervix
33	chr17:17865000-17869800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr17:17865800-17873200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr17:17866600-17874400	Enhancers	Fetal Heart	heart
36	chr17:17866800-17869800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr17:17866800-17874200	Weak transcription	K562	blood
38	chr17:17867000-17871000	Weak transcription	Primary T cells fromperipheralblood	blood
39	chr17:17867000-17874000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr17:17867000-17874200	Weak transcription	Monocytes-CD14+_RO01746	blood
41	chr17:17867200-17871400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr17:17867200-17874000	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr17:17867400-17869800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr17:17867400-17873800	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr17:17867600-17872800	Weak transcription	Pancreatic Islets	Pancreatic Islet
46	chr17:17867600-17873800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr17:17867600-17873800	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr17:17867600-17874200	Weak transcription	Fetal Kidney	kidney
49	chr17:17867800-17870200	Weak transcription	Primary T cells from cord blood	blood
50	chr17:17867800-17872600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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