Variant report

Variant	rs12600546
Chromosome Location	chr17:17867614-17867615
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:17862264..17864239-chr17:17866031..17867692,2	MCF-7	breast:
2	chr17:17867285..17871471-chr17:17874516..17877381,4	MCF-7	breast:
3	chr17:17861929..17864204-chr17:17866706..17869087,2	K562	blood:
4	chr17:17861024..17862929-chr17:17866767..17869059,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000171962	Chromatin interaction
ENSG00000175662	Chromatin interaction

Extended variants
information (count: 132 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:126)

rs_ID	r²[population]
rs10048206	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1052299	0.83[CEU][hapmap]
rs11078400	0.91[CEU][hapmap];0.92[CHB][hapmap]
rs11078403	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11078404	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11078405	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11078406	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11078407	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11078408	0.92[JPT][hapmap];0.84[EUR][1000 genomes]
rs1108648	0.81[CEU][hapmap]
rs11650649	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs11650890	0.88[EUR][1000 genomes]
rs11656840	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11657773	0.85[EUR][1000 genomes]
rs11657845	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11869536	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11870660	0.83[EUR][1000 genomes]
rs11871899	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12452219	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12452254	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12603148	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12941039	0.91[CEU][hapmap]
rs12943500	0.91[CEU][hapmap]
rs12953299	0.80[CEU][hapmap]
rs16960744	0.83[CEU][hapmap];0.83[CHB][hapmap];0.96[YRI][hapmap]
rs2236513	0.82[CEU][hapmap]
rs2350977	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28428991	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2955354	0.84[JPT][hapmap]
rs2955359	0.92[JPT][hapmap]
rs2955370	0.83[JPT][hapmap]
rs2955371	0.91[CEU][hapmap]
rs2955372	0.92[JPT][hapmap]
rs2955377	0.92[JPT][hapmap]
rs2955380	0.92[JPT][hapmap]
rs2955381	0.83[JPT][hapmap]
rs2955382	0.82[CEU][hapmap]
rs2955384	0.92[JPT][hapmap]
rs2955385	0.92[JPT][hapmap]
rs3183702	0.87[CEU][hapmap]
rs4077198	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4077828	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4244602	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4257260	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4299203	0.83[EUR][1000 genomes]
rs4321247	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4341796	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4343339	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4368210	0.92[JPT][hapmap]
rs4413022	1.00[CEU][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4414547	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4470201	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4471742	0.84[EUR][1000 genomes]
rs4506969	0.84[JPT][hapmap]
rs4534911	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4553680	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4584886	0.92[JPT][hapmap]
rs4616340	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4924823	0.91[CEU][hapmap];0.92[CHB][hapmap]
rs4925120	0.83[CEU][hapmap];0.83[CHB][hapmap];0.96[YRI][hapmap]
rs4925123	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs4925125	0.95[CEU][hapmap];0.91[CHB][hapmap];0.90[EUR][1000 genomes]
rs4925126	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4925129	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4925130	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs5002487	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs57728924	0.83[EUR][1000 genomes]
rs59304093	0.80[EUR][1000 genomes]
rs62064156	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62064158	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62072049	0.83[EUR][1000 genomes]
rs6502619	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs6502622	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[YRI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6502624	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6502625	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs6502626	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6502627	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6502629	0.91[CEU][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs66531105	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs67253360	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7207043	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7207395	0.94[EUR][1000 genomes]
rs7207821	0.84[JPT][hapmap]
rs7208190	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7213225	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7214002	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7214536	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7219320	0.83[EUR][1000 genomes]
rs7222480	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7224815	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs7406982	0.92[JPT][hapmap]
rs7503334	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs8065416	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8065563	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs8065970	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8066982	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8068175	0.83[EUR][1000 genomes]
rs8068820	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8070128	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8070722	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8070748	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8073001	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8075965	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8076747	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8077338	0.81[EUR][1000 genomes]
rs8077530	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8078105	1.00[CEU][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8078138	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8078583	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8079321	0.91[CEU][hapmap];0.92[CHB][hapmap]
rs8080061	0.91[CEU][hapmap];0.92[CHB][hapmap];0.96[YRI][hapmap]
rs8080823	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs950966	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs9635697	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9635698	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9890341	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9896837	0.92[JPT][hapmap]
rs9904163	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9905284	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9907246	0.91[CEU][hapmap]
rs9907287	0.91[CEU][hapmap];0.92[CHB][hapmap]
rs9908832	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9912895	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[YRI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9913724	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9914127	0.84[EUR][1000 genomes]
rs9915248	0.83[CEU][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12600546	SREBF1	cis	Whole Blood	GTEx

Chromatin state (count:97 , 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	chr17:17862400-17868600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr17:17862400-17874200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr17:17862600-17868600	Weak transcription	Esophagus	oesophagus
5	chr17:17863200-17868600	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr17:17863400-17874000	Weak transcription	NH-A	brain
7	chr17:17863600-17869800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr17:17863600-17873800	Weak transcription	HSMMtube	muscle
9	chr17:17863800-17867800	Weak transcription	Ovary	ovary
10	chr17:17863800-17868200	Weak transcription	Colon Smooth Muscle	Colon
11	chr17:17863800-17868200	Weak transcription	Right Atrium	heart
12	chr17:17863800-17868400	Weak transcription	Right Ventricle	heart
13	chr17:17863800-17869400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr17:17863800-17869800	Weak transcription	Fetal Thymus	thymus
15	chr17:17863800-17871800	Weak transcription	Fetal Brain Male	brain
16	chr17:17863800-17872800	Weak transcription	Brain Germinal Matrix	brain
17	chr17:17863800-17873800	Weak transcription	Fetal Muscle Leg	muscle
18	chr17:17863800-17873800	Weak transcription	Thymus	Thymus
19	chr17:17863800-17874400	Weak transcription	Fetal Muscle Trunk	muscle
20	chr17:17864000-17868000	Weak transcription	Fetal Stomach	stomach
21	chr17:17864000-17868200	Weak transcription	Lung	lung
22	chr17:17864000-17868600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr17:17864000-17868600	Weak transcription	Liver	Liver
24	chr17:17864000-17868600	Weak transcription	Gastric	stomach
25	chr17:17864000-17868600	Weak transcription	Stomach Smooth Muscle	stomach
26	chr17:17864000-17870400	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr17:17864000-17873800	Weak transcription	HSMM	muscle
28	chr17:17864000-17874200	Weak transcription	Placenta	Placenta
29	chr17:17864000-17874400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr17:17864000-17874400	Weak transcription	Pancreas	Pancrea
31	chr17:17864200-17868600	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr17:17864200-17868800	Weak transcription	GM12878-XiMat	blood
33	chr17:17864200-17869600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr17:17864200-17869600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr17:17864200-17869800	Weak transcription	NHDF-Ad	bronchial
36	chr17:17864200-17871400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr17:17864200-17873600	Weak transcription	NHEK	skin
38	chr17:17864200-17873800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr17:17864200-17873800	Weak transcription	Duodenum Mucosa	Duodenum
40	chr17:17864200-17873800	Weak transcription	Fetal Intestine Large	intestine
41	chr17:17864200-17874000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr17:17864200-17874200	Weak transcription	Fetal Intestine Small	intestine
43	chr17:17864200-17874200	Weak transcription	Rectal Smooth Muscle	rectum
44	chr17:17864400-17868600	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr17:17864400-17872800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
46	chr17:17864400-17872800	Weak transcription	A549	lung
47	chr17:17864400-17873800	Weak transcription	Stomach Mucosa	stomach
48	chr17:17864400-17874400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr17:17864600-17869000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr17:17864600-17869000	Weak transcription	Primary T killer memory cells from peripheral blood	blood

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