Variant report

Variant	rs4244602
Chromosome Location	chr17:17841456-17841457
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:17835824..17837340-chr17:17839112..17841856,2	K562	blood:
2	chr17:17835824..17837359-chr17:17839112..17843100,3	K562	blood:
3	chr17:17840484..17842784-chr17:17877898..17879445,2	MCF-7	breast:
4	chr17:17830467..17833990-chr17:17840176..17843911,4	MCF-7	breast:

Extended variants
information (count: 142 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:137)

rs_ID	r²[population]
rs10048206	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1052299	0.83[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap]
rs11078400	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs11078403	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11078404	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11078405	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11078406	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11078407	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11078408	0.81[EUR][1000 genomes]
rs1108648	0.81[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap]
rs11650649	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11650890	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11652881	0.82[JPT][hapmap]
rs11656665	0.82[JPT][hapmap]
rs11656840	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11657074	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11657423	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs11657773	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11657845	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11658309	0.82[AMR][1000 genomes]
rs11869536	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11870660	0.82[EUR][1000 genomes]
rs11871899	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12452219	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12452254	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12600546	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12603148	0.96[EUR][1000 genomes]
rs12936037	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12941039	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12943500	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12953299	0.80[CEU][hapmap];1.00[CHB][hapmap]
rs16960744	0.83[CEU][hapmap]
rs1889014	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1889018	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs2236513	0.83[CEU][hapmap];0.82[JPT][hapmap]
rs2350976	0.82[JPT][hapmap]
rs2350977	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28428991	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2955371	0.91[CEU][hapmap];0.82[JPT][hapmap]
rs2955382	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs3183702	0.87[CEU][hapmap];0.82[JPT][hapmap]
rs35451946	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3744115	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs3818717	0.82[JPT][hapmap]
rs4077198	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4077828	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4257260	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4299203	0.82[EUR][1000 genomes]
rs4321247	0.91[EUR][1000 genomes]
rs4341796	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4343339	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4413022	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4414547	0.96[EUR][1000 genomes]
rs4470201	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4471742	0.82[EUR][1000 genomes]
rs4534911	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4553680	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4616340	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4924822	0.82[JPT][hapmap]
rs4924823	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs4925120	0.83[CEU][hapmap]
rs4925123	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4925125	0.95[CEU][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4925126	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4925129	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4925130	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4925138	0.82[JPT][hapmap]
rs5002487	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57728924	0.82[EUR][1000 genomes]
rs62064156	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62064158	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62072049	0.85[EUR][1000 genomes]
rs6502619	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6502622	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6502624	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6502625	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]
rs6502626	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6502627	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6502629	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66531105	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs67253360	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7207043	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7207395	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7208190	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7213225	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7214002	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7214536	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7219320	0.81[EUR][1000 genomes]
rs7222480	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7224815	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.85[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	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8065416	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8065497	0.91[ASN][1000 genomes]
rs8065563	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8065970	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8066982	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8068175	0.82[EUR][1000 genomes]
rs8068820	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8070128	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8070624	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8070722	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8070748	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8073001	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs8075965	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8076747	0.94[EUR][1000 genomes]
rs8077338	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8077530	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8078105	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8078138	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8078583	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8079321	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs8080061	0.91[CEU][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8080823	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs854762	0.82[JPT][hapmap]
rs854764	0.82[JPT][hapmap]
rs854766	0.82[JPT][hapmap]
rs950966	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9635697	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9635698	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9890341	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9891957	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs9895750	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9899634	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs9902941	0.82[JPT][hapmap]
rs9904163	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9905284	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9907246	0.91[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.89[YRI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9907287	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs9908017	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9908299	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9908832	0.95[EUR][1000 genomes]
rs9912895	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9913724	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9914127	0.81[EUR][1000 genomes]
rs9915248	0.83[CEU][hapmap];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
rs4244602	SREBF1	cis	Whole Blood	GTEx

Chromatin state (count:109 , 50 per page) page: 1 2 3

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	chr17:17832400-17843600	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr17:17832800-17843600	Weak transcription	Fetal Muscle Trunk	muscle
5	chr17:17833000-17843600	Weak transcription	Fetal Stomach	stomach
6	chr17:17835000-17843800	Weak transcription	Aorta	Aorta
7	chr17:17836400-17841800	Enhancers	Primary T helper cells PMA-I stimulated	--
8	chr17:17836400-17841800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
9	chr17:17836400-17842000	Enhancers	Sigmoid Colon	Sigmoid Colon
10	chr17:17836400-17842600	Enhancers	NHDF-Ad	bronchial
11	chr17:17836400-17853000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr17:17836600-17846600	Enhancers	Skeletal Muscle Female	skeletal muscle
13	chr17:17836800-17841800	Enhancers	NH-A	brain
14	chr17:17836800-17842600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr17:17836800-17842600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr17:17836800-17843800	Enhancers	Osteobl	bone
17	chr17:17836800-17846000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr17:17837000-17845400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr17:17837400-17842400	Enhancers	Brain Anterior Caudate	brain
20	chr17:17837400-17842600	Enhancers	Brain Hippocampus Middle	brain
21	chr17:17837400-17847800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr17:17837600-17841600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr17:17837600-17841600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr17:17837600-17841800	Enhancers	Lung	lung
25	chr17:17837600-17842000	Enhancers	Brain Inferior Temporal Lobe	brain
26	chr17:17837600-17842400	Enhancers	Left Ventricle	heart
27	chr17:17837600-17842600	Enhancers	Placenta	Placenta
28	chr17:17837800-17844000	Enhancers	Fetal Heart	heart
29	chr17:17837800-17847600	Enhancers	HMEC	breast
30	chr17:17838000-17841800	Enhancers	Brain Angular Gyrus	brain
31	chr17:17838000-17842600	Enhancers	Brain Substantia Nigra	brain
32	chr17:17838000-17844400	Enhancers	Fetal Intestine Large	intestine
33	chr17:17838000-17845000	Enhancers	Right Ventricle	heart
34	chr17:17838000-17848600	Enhancers	Duodenum Smooth Muscle	Duodenum
35	chr17:17838200-17841600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr17:17838200-17841600	Enhancers	Pancreas	Pancrea
37	chr17:17838200-17841600	Enhancers	Spleen	Spleen
38	chr17:17838200-17841800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
39	chr17:17838200-17842000	Enhancers	Brain Cingulate Gyrus	brain
40	chr17:17838200-17842400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr17:17838200-17842600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr17:17838200-17843000	Enhancers	Fetal Intestine Small	intestine
43	chr17:17838200-17844600	Enhancers	Rectal Mucosa Donor 31	rectum
44	chr17:17838200-17845600	Enhancers	Right Atrium	heart
45	chr17:17838400-17842400	Enhancers	Skeletal Muscle Male	skeletal muscle
46	chr17:17838400-17842800	Enhancers	Rectal Mucosa Donor 29	rectum
47	chr17:17838400-17844800	Enhancers	Small Intestine	intestine
48	chr17:17838600-17842600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr17:17838600-17842800	Enhancers	HepG2	liver
50	chr17:17838600-17845400	Enhancers	Esophagus	oesophagus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links