Variant report

Variant	rs17210963
Chromosome Location	chr3:98497659-98497660
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MYBL2	chr3:98497404-98498176	HepG2	liver:	n/a	n/a
2	SP1	chr3:98497531-98498101	HepG2	liver:	n/a	n/a
3	RFX5	chr3:98497527-98497985	HepG2	liver:	n/a	n/a
4	CEBPD	chr3:98497645-98498006	HepG2	liver:	n/a	chr3:98497807-98497818
5	TEAD4	chr3:98497431-98498146	HepG2	liver:	n/a	n/a
6	CEBPB	chr3:98497433-98498077	HepG2	liver:	n/a	chr3:98497806-98497817
7	MYC	chr3:98497587-98498325	MCF10A-Er-Src	breast:	n/a	chr3:98498010-98498023 chr3:98498012-98498021 chr3:98498011-98498022
8	FOS	chr3:98497286-98498328	MCF10A-Er-Src	breast:	n/a	n/a
9	EP300	chr3:98497453-98498155	HepG2	liver:	n/a	chr3:98498036-98498050
10	CEBPB	chr3:98497512-98497998	HepG2	liver:	n/a	chr3:98497806-98497817
11	STAT3	chr3:98497629-98498357	MCF10A-Er-Src	breast:	n/a	n/a
12	CEBPB	chr3:98497637-98497951	A549	lung:	n/a	chr3:98497806-98497817
13	CEBPB	chr3:98497623-98497986	K562	blood:	n/a	chr3:98497806-98497817
14	MAFK	chr3:98497447-98497894	HepG2	liver:	n/a	n/a
15	FOXA1	chr3:98497477-98498124	HepG2	liver:	n/a	n/a
16	FOXA1	chr3:98497620-98498121	HepG2	liver:	n/a	n/a
17	STAT3	chr3:98497437-98498221	MCF10A-Er-Src	breast:	n/a	n/a
18	POLR2A	chr3:98497655-98498431	HUVEC	blood vessel:	n/a	n/a
19	NFIC	chr3:98497552-98498458	SK-N-SH	brain:	n/a	n/a
20	MYBL2	chr3:98497517-98498123	HepG2	liver:	n/a	n/a
21	NFIC	chr3:98497472-98498061	HepG2	liver:	n/a	n/a
22	FOXA1	chr3:98497519-98498027	HepG2	liver:	n/a	n/a
23	POLR2A	chr3:98497193-98498558	U87	brain:	n/a	n/a
24	NFIC	chr3:98497464-98498048	HepG2	liver:	n/a	n/a
25	PBX3	chr3:98497497-98498359	SK-N-SH	brain:	n/a	n/a
26	FOS	chr3:98497184-98498296	MCF10A-Er-Src	breast:	n/a	n/a
27	MAFK	chr3:98497037-98497887	IMR90	lung:	n/a	chr3:98497336-98497351
28	POLR2A	chr3:98497575-98498061	SK-N-SH	brain:	n/a	n/a
29	CEBPB	chr3:98497593-98497989	MCF-7	breast:	n/a	chr3:98497806-98497817
30	ARID3A	chr3:98497516-98498094	HepG2	liver:	n/a	n/a
31	FOXA2	chr3:98497535-98498007	HepG2	liver:	n/a	n/a
32	STAT3	chr3:98497639-98497998	MCF10A-Er-Src	breast:	n/a	n/a
33	POLR2A	chr3:98497605-98497790	HepG2	liver:	n/a	n/a
34	JUND	chr3:98497623-98498292	HepG2	liver:	n/a	n/a
35	HDAC2	chr3:98497563-98498056	HepG2	liver:	n/a	n/a
36	HDAC2	chr3:98497337-98498125	HepG2	liver:	n/a	n/a
37	HNF4A	chr3:98497621-98498052	HepG2	liver:	n/a	n/a
38	MAZ	chr3:98497595-98497974	HepG2	liver:	n/a	n/a
39	MXI1	chr3:98497578-98498202	HepG2	liver:	n/a	n/a
40	HNF4A	chr3:98497656-98498264	HepG2	liver:	n/a	n/a
41	EP300	chr3:98497491-98498102	HepG2	liver:	n/a	chr3:98498036-98498050
42	STAT3	chr3:98497643-98498124	MCF10A-Er-Src	breast:	n/a	n/a
43	FOXA1	chr3:98497609-98498049	HepG2	liver:	n/a	n/a
44	RUNX3	chr3:98497142-98497663	GM12878	blood:	n/a	n/a
45	REST	chr3:98497640-98497982	HepG2	liver:	n/a	n/a
46	POLR2A	chr3:98496882-98498523	U87	brain:	n/a	n/a
47	FOS	chr3:98497583-98498265	MCF10A-Er-Src	breast:	n/a	n/a
48	BHLHE40	chr3:98497540-98498118	HepG2	liver:	n/a	n/a
49	GATA3	chr3:98497479-98498320	SK-N-SH	brain:	n/a	n/a
50	HNF4G	chr3:98497534-98498125	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:98494773..98497684-chr3:98500222..98503484,3	K562	blood:

Variant related genes	Relation type
PDLIM1P4	TF binding region
ST3GAL6	TF binding region
ENSG00000064225	Chromatin interaction
ENSG00000249274	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10433438	0.93[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.89[EUR][1000 genomes]
rs10511169	0.93[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap]
rs10935518	0.93[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.88[EUR][1000 genomes]
rs10935542	0.87[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap]
rs11716579	0.91[EUR][1000 genomes]
rs11914715	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11916285	0.93[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12203	0.93[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1440154	0.93[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16840260	1.00[CHB][hapmap];0.82[JPT][hapmap];0.89[EUR][1000 genomes]
rs16846347	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17278047	0.93[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17852693	0.89[EUR][1000 genomes]
rs1822017	0.87[CEU][hapmap];0.85[JPT][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1827158	0.93[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.90[EUR][1000 genomes]
rs2278599	0.93[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3772100	0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55650073	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs55662129	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs55730510	0.89[EUR][1000 genomes]
rs55988144	0.89[EUR][1000 genomes]
rs56075614	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56290036	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56322058	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6440159	0.93[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6805605	0.93[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73136038	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73136045	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73136048	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73136057	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73136060	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73138004	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73138027	0.93[EUR][1000 genomes]
rs73138030	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73138048	0.91[EUR][1000 genomes]
rs73138053	0.91[EUR][1000 genomes]
rs73138055	0.91[EUR][1000 genomes]
rs73138058	0.91[EUR][1000 genomes]
rs73138063	0.88[EUR][1000 genomes]
rs73138082	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73140009	0.90[EUR][1000 genomes]
rs7614892	0.93[EUR][1000 genomes]
rs7629550	0.87[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap]
rs7644946	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8179927	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]

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	esv3390386	chr3:98174549-98579953	Genic enhancers Strong transcription Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv591065	chr3:98204198-98766326	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1007140	chr3:98421229-99202458	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv536663	chr3:98421229-99202458	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv877214	chr3:98445324-98738006	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98478800-98515200	Weak transcription	HUES64 Cell Line	embryonic stem cell
2	chr3:98482600-98501800	Weak transcription	Fetal Stomach	stomach
3	chr3:98483000-98517600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr3:98483200-98518000	Weak transcription	Stomach Smooth Muscle	stomach
5	chr3:98483600-98513600	Weak transcription	Brain Germinal Matrix	brain
6	chr3:98483800-98515000	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr3:98484000-98498000	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr3:98484000-98514000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr3:98484200-98515200	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr3:98484800-98529800	Weak transcription	Primary B cells from cord blood	blood
11	chr3:98489800-98503000	Weak transcription	Psoas Muscle	Psoas
12	chr3:98490200-98525200	Weak transcription	Rectal Smooth Muscle	rectum
13	chr3:98492200-98517800	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr3:98493800-98498400	Enhancers	HepG2	liver
15	chr3:98493800-98499600	Enhancers	Fetal Intestine Large	intestine
16	chr3:98494400-98498400	Enhancers	Fetal Intestine Small	intestine
17	chr3:98494600-98499200	Genic enhancers	Primary monocytes fromperipheralblood	blood
18	chr3:98494600-98506000	Enhancers	Aorta	Aorta
19	chr3:98495200-98498000	Enhancers	Pancreas	Pancrea
20	chr3:98495800-98497800	Enhancers	HUVEC	blood vessel
21	chr3:98495800-98498000	Enhancers	Gastric	stomach
22	chr3:98495800-98499200	Enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr3:98495800-98499600	Enhancers	Cortex derived primary cultured neurospheres	brain
24	chr3:98496000-98497800	Enhancers	Fetal Heart	heart
25	chr3:98496000-98498000	Enhancers	Stomach Mucosa	stomach
26	chr3:98496000-98499200	Enhancers	NHLF	lung
27	chr3:98496000-98499600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr3:98496000-98499600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr3:98496000-98499800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr3:98496000-98499800	Enhancers	NH-A	brain
31	chr3:98496200-98497800	Enhancers	NHDF-Ad	bronchial
32	chr3:98496200-98498200	Enhancers	Liver	Liver
33	chr3:98496200-98498600	Enhancers	Skeletal Muscle Male	skeletal muscle
34	chr3:98496200-98498800	Enhancers	Brain Hippocampus Middle	brain
35	chr3:98496200-98499000	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
36	chr3:98496200-98499200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr3:98496200-98499400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr3:98496200-98499600	Enhancers	Brain Cingulate Gyrus	brain
39	chr3:98496200-98499800	Enhancers	Brain Substantia Nigra	brain
40	chr3:98496400-98498200	Enhancers	Fetal Lung	lung
41	chr3:98496400-98498800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr3:98496400-98499400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr3:98496400-98499800	Enhancers	Brain Anterior Caudate	brain
44	chr3:98496600-98499600	Enhancers	Adipose Nuclei	Adipose
45	chr3:98496600-98503800	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr3:98496800-98498600	Enhancers	Right Atrium	heart
47	chr3:98496800-98499200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr3:98496800-98499200	Enhancers	Skeletal Muscle Female	skeletal muscle
49	chr3:98496800-98502800	Weak transcription	Fetal Thymus	thymus
50	chr3:98497000-98498200	Enhancers	Primary hematopoietic stem cells	blood

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