Variant report

Variant	rs6502625
Chromosome Location	chr17:17848286-17848287
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:17583605..17586446-chr17:17846960..17849199,2	K562	blood:
2	chr17:17791829..17793530-chr17:17846547..17848415,2	K562	blood:
3	chr17:17846210..17848871-chr17:17854659..17856269,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000108557	Chromatin interaction

Extended variants
information (count: 129 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:124)

rs_ID	r²[population]
rs10048206	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs1052299	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs11078400	0.87[CEU][hapmap]
rs11078403	0.83[EUR][1000 genomes]
rs11078404	0.88[EUR][1000 genomes]
rs11078405	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11078406	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs11078407	0.89[EUR][1000 genomes]
rs1108648	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs11650649	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11650890	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11652881	0.82[JPT][hapmap]
rs11656665	0.82[JPT][hapmap]
rs11656840	0.95[CEU][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11657074	0.91[ASN][1000 genomes]
rs11657423	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs11657773	0.80[EUR][1000 genomes]
rs11657845	0.81[EUR][1000 genomes]
rs11869536	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11871899	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12452219	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12452254	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12600546	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs12603148	0.88[EUR][1000 genomes]
rs12936037	0.91[ASN][1000 genomes]
rs12941039	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12943500	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12953299	1.00[CHB][hapmap]
rs1889014	0.84[CEU][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1889018	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs2236513	0.82[JPT][hapmap]
rs2350976	0.82[JPT][hapmap]
rs2350977	0.96[CEU][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28428991	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2955371	0.87[CEU][hapmap];0.82[JPT][hapmap]
rs2955382	0.87[CEU][hapmap];1.00[JPT][hapmap]
rs3183702	0.83[CEU][hapmap];0.82[JPT][hapmap]
rs3744115	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs3818717	0.82[JPT][hapmap]
rs4077198	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4077828	0.96[CEU][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4244602	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4257260	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs4321247	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4341796	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4343339	0.87[EUR][1000 genomes]
rs4413022	0.95[CEU][hapmap];0.88[EUR][1000 genomes]
rs4414547	0.88[EUR][1000 genomes]
rs4470201	0.96[CEU][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4534911	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4553680	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4616340	0.88[EUR][1000 genomes]
rs4924822	0.82[JPT][hapmap]
rs4924823	0.87[CEU][hapmap]
rs4925123	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4925125	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs4925126	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs4925129	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4925130	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4925138	0.83[CEU][hapmap];0.82[JPT][hapmap]
rs5002487	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62064156	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62064158	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6502619	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6502622	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6502624	0.96[CEU][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6502626	0.89[EUR][1000 genomes]
rs6502627	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs6502629	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]
rs66531105	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs67253360	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7207043	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7207395	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7208190	0.86[EUR][1000 genomes]
rs7213225	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs7214002	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs7214536	0.89[EUR][1000 genomes]
rs7222480	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7224815	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7359509	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs7501812	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs7503334	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8065416	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs8065497	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8065563	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8065970	0.88[EUR][1000 genomes]
rs8066982	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs8068820	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8070128	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8070624	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8070722	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8070748	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs8073001	0.96[CEU][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8075965	0.86[EUR][1000 genomes]
rs8076747	0.86[EUR][1000 genomes]
rs8077338	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8077530	0.86[EUR][1000 genomes]
rs8078105	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs8078138	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8078583	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8079321	0.87[CEU][hapmap]
rs8080061	0.87[CEU][hapmap]
rs8080823	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs854762	0.83[CEU][hapmap];0.82[JPT][hapmap]
rs854764	0.83[CEU][hapmap];0.82[JPT][hapmap]
rs854765	0.83[CEU][hapmap]
rs854766	0.83[CEU][hapmap];0.82[JPT][hapmap]
rs950966	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9635697	0.88[EUR][1000 genomes]
rs9635698	0.87[EUR][1000 genomes]
rs9890341	0.96[CEU][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9891957	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs9895750	0.91[ASN][1000 genomes]
rs9899634	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs9902941	0.82[JPT][hapmap]
rs9904163	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9905284	0.88[EUR][1000 genomes]
rs9907246	0.87[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs9907287	0.87[CEU][hapmap]
rs9908299	0.91[ASN][1000 genomes]
rs9908832	0.86[EUR][1000 genomes]
rs9912895	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9913724	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9915248	1.00[CHB][hapmap];0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6502625	SREBF1	cis	Whole Blood	GTEx

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:17828200-17861000	Weak transcription	Primary B cells from cord blood	blood
2	chr17:17828600-17858000	Weak transcription	Primary B cells from peripheral blood	blood
3	chr17:17836400-17853000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr17:17838000-17848600	Enhancers	Duodenum Smooth Muscle	Duodenum
5	chr17:17839400-17858800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr17:17839400-17860200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr17:17839800-17859800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr17:17843000-17848400	Enhancers	NHLF	lung
9	chr17:17843200-17848400	Enhancers	Left Ventricle	heart
10	chr17:17843200-17848600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr17:17843400-17848600	Enhancers	Ovary	ovary
12	chr17:17843400-17849000	Enhancers	Fetal Lung	lung
13	chr17:17843600-17848400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr17:17843600-17848400	Enhancers	Brain Inferior Temporal Lobe	brain
15	chr17:17843600-17848600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr17:17843800-17848400	Enhancers	Lung	lung
17	chr17:17843800-17849000	Enhancers	Brain Anterior Caudate	brain
18	chr17:17844400-17848800	Enhancers	Fetal Heart	heart
19	chr17:17844800-17859800	Weak transcription	Colonic Mucosa	Colon
20	chr17:17844800-17861400	Weak transcription	Liver	Liver
21	chr17:17845400-17849000	Enhancers	HepG2	liver
22	chr17:17845400-17849600	Enhancers	Fetal Intestine Large	intestine
23	chr17:17845800-17848400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr17:17846000-17848600	Enhancers	Colon Smooth Muscle	Colon
25	chr17:17846000-17848600	Enhancers	Rectal Smooth Muscle	rectum
26	chr17:17846000-17848800	Enhancers	Fetal Stomach	stomach
27	chr17:17846000-17849600	Enhancers	Right Ventricle	heart
28	chr17:17846000-17849800	Enhancers	Fetal Intestine Small	intestine
29	chr17:17846400-17848400	Enhancers	Brain Germinal Matrix	brain
30	chr17:17846400-17848400	Enhancers	Fetal Muscle Leg	muscle
31	chr17:17846600-17848400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr17:17846600-17848400	Enhancers	Primary T helper cells PMA-I stimulated	--
33	chr17:17846600-17848800	Enhancers	Stomach Smooth Muscle	stomach
34	chr17:17847000-17848800	Enhancers	Muscle Satellite Cultured Cells	--
35	chr17:17847000-17848800	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr17:17847000-17850800	Enhancers	Skeletal Muscle Female	skeletal muscle
37	chr17:17847000-17858000	Weak transcription	Adipose Nuclei	Adipose
38	chr17:17847000-17860200	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr17:17847200-17850400	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr17:17847200-17854000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr17:17847200-17861400	Weak transcription	Fetal Kidney	kidney
42	chr17:17847400-17848400	Enhancers	Fetal Muscle Trunk	muscle
43	chr17:17847400-17848800	Enhancers	Fetal Brain Female	brain
44	chr17:17847400-17849000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr17:17847400-17849600	Weak transcription	Osteobl	bone
46	chr17:17847400-17850400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr17:17847400-17850600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr17:17847400-17851000	Enhancers	Skeletal Muscle Male	skeletal muscle
49	chr17:17847400-17852400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr17:17847400-17856000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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