Variant report

Variant	rs3755576
Chromosome Location	chr3:98497029-98497030
allele	A/G
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	ZEB1	chr3:98495890-98497201	HepG2	liver:	n/a	chr3:98497020-98497032
2	NFIC	chr3:98496471-98497060	SK-N-SH	brain:	n/a	n/a
3	POLR2A	chr3:98496882-98498523	U87	brain:	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
ENSG00000249274	Chromatin interaction
ENSG00000064225	Chromatin interaction

Extended variants
information (count: 114 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:109)

rs_ID	r²[population]
rs1062196	0.96[CEU][hapmap];0.88[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12107050	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12330170	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12490832	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13060012	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs14310	0.83[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1440150	1.00[CEU][hapmap];0.83[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1440151	0.83[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1440152	0.88[CEU][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1440153	0.97[GIH][hapmap];0.89[TSI][hapmap]
rs17270593	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17270986	0.80[CHD][hapmap]
rs1837500	0.96[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs1866677	0.87[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1866678	0.88[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1866679	0.90[ASN][1000 genomes]
rs1967009	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs2119187	1.00[CEU][hapmap];0.88[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.84[EUR][1000 genomes]
rs2119188	0.93[CHB][hapmap];0.96[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs2279761	0.82[EUR][1000 genomes]
rs2290067	1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2334230	1.00[CEU][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.92[LWK][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2439214	0.87[EUR][1000 genomes]
rs2439217	0.88[EUR][1000 genomes]
rs2439220	0.84[EUR][1000 genomes]
rs2439222	0.88[CHB][hapmap];0.96[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap]
rs2439223	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs2439224	0.80[CHD][hapmap]
rs2439226	0.84[EUR][1000 genomes]
rs2439228	0.81[ASN][1000 genomes]
rs2439229	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2439231	0.88[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2439236	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs2454673	0.96[CEU][hapmap];0.88[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.83[EUR][1000 genomes]
rs2454676	0.91[EUR][1000 genomes]
rs2454677	0.90[EUR][1000 genomes]
rs2454678	0.84[EUR][1000 genomes]
rs2454680	0.84[EUR][1000 genomes]
rs2454682	0.83[CHB][hapmap];0.96[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap]
rs2454684	0.87[EUR][1000 genomes]
rs2454685	0.88[CHB][hapmap];0.96[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap]
rs2454691	0.83[EUR][1000 genomes]
rs2470857	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs2470859	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs2470860	0.86[EUR][1000 genomes]
rs2470861	0.96[CEU][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs2470864	0.92[EUR][1000 genomes]
rs2470865	0.92[EUR][1000 genomes]
rs2470867	1.00[CEU][hapmap];0.88[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2470869	0.88[CHB][hapmap];0.96[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2470879	0.82[ASN][1000 genomes]
rs2470881	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs2470885	0.96[CEU][hapmap];0.88[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.83[EUR][1000 genomes]
rs28802000	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2919234	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2919236	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34234373	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34558202	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3755574	1.00[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs3772098	1.00[CEU][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3772099	1.00[CEU][hapmap];0.84[JPT][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3772101	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3772102	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3821359	1.00[CEU][hapmap];0.86[JPT][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4269027	0.80[EUR][1000 genomes]
rs4425200	1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4425201	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.98[TSI][hapmap];0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4426625	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4426626	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4494869	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62278486	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6782630	0.88[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6785935	1.00[CEU][hapmap];0.88[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6788418	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6788689	0.88[ASN][1000 genomes]
rs6790650	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6804850	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6808116	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs704585	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7431448	1.00[CEU][hapmap];1.00[GIH][hapmap];0.92[LWK][hapmap];0.93[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7611929	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7612036	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7612605	0.91[EUR][1000 genomes]
rs7616275	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7630800	0.84[EUR][1000 genomes]
rs828609	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs844160	0.96[CEU][hapmap];0.86[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9289683	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs9289685	0.83[EUR][1000 genomes]
rs9811305	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9811449	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9811860	0.88[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs9814819	0.88[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs9815226	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9820384	0.84[EUR][1000 genomes]
rs9823430	0.88[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs9843214	1.00[CEU][hapmap];0.88[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap]
rs9845558	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9855175	0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9860216	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9866570	1.00[CEU][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9867586	0.83[ASN][1000 genomes]
rs9872152	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9873932	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9878392	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9881519	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9883516	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9883537	1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs999147	1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.94[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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3755576	ST3GAL6	Cis_1M	lymphoblastoid	RTeQTL
rs3755576	ST3GAL6	cis	multi-tissue	Pritchard

Chromatin state (count:80 , 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	chr3:98482800-98497400	Weak transcription	Fetal Muscle Leg	muscle
4	chr3:98483000-98497400	Weak transcription	Spleen	Spleen
5	chr3:98483000-98517600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr3:98483200-98518000	Weak transcription	Stomach Smooth Muscle	stomach
7	chr3:98483600-98513600	Weak transcription	Brain Germinal Matrix	brain
8	chr3:98483800-98515000	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr3:98484000-98498000	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr3:98484000-98514000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr3:98484200-98515200	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr3:98484800-98529800	Weak transcription	Primary B cells from cord blood	blood
13	chr3:98488600-98497200	Strong transcription	Primary neutrophils fromperipheralblood	blood
14	chr3:98488600-98497200	Weak transcription	Fetal Kidney	kidney
15	chr3:98489800-98497400	Weak transcription	Right Ventricle	heart
16	chr3:98489800-98497600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr3:98489800-98503000	Weak transcription	Psoas Muscle	Psoas
18	chr3:98490200-98525200	Weak transcription	Rectal Smooth Muscle	rectum
19	chr3:98490400-98497400	Weak transcription	Fetal Brain Female	brain
20	chr3:98491600-98497400	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr3:98492200-98517800	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr3:98493800-98498400	Enhancers	HepG2	liver
23	chr3:98493800-98499600	Enhancers	Fetal Intestine Large	intestine
24	chr3:98494400-98497200	Genic enhancers	Monocytes-CD14+_RO01746	blood
25	chr3:98494400-98498400	Enhancers	Fetal Intestine Small	intestine
26	chr3:98494600-98497600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr3:98494600-98499200	Genic enhancers	Primary monocytes fromperipheralblood	blood
28	chr3:98494600-98506000	Enhancers	Aorta	Aorta
29	chr3:98495200-98497600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr3:98495200-98498000	Enhancers	Pancreas	Pancrea
31	chr3:98495400-98497200	Enhancers	Pancreatic Islets	Pancreatic Islet
32	chr3:98495600-98497200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr3:98495600-98497200	Enhancers	HMEC	breast
34	chr3:98495800-98497400	Enhancers	Osteobl	bone
35	chr3:98495800-98497800	Enhancers	HUVEC	blood vessel
36	chr3:98495800-98498000	Enhancers	Gastric	stomach
37	chr3:98495800-98499200	Enhancers	Breast Myoepithelial Primary Cells	Breast
38	chr3:98495800-98499600	Enhancers	Cortex derived primary cultured neurospheres	brain
39	chr3:98496000-98497200	Enhancers	Brain Angular Gyrus	brain
40	chr3:98496000-98497400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr3:98496000-98497400	Enhancers	Muscle Satellite Cultured Cells	--
42	chr3:98496000-98497800	Enhancers	Fetal Heart	heart
43	chr3:98496000-98498000	Enhancers	Stomach Mucosa	stomach
44	chr3:98496000-98499200	Enhancers	NHLF	lung
45	chr3:98496000-98499600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr3:98496000-98499600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr3:98496000-98499800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr3:98496000-98499800	Enhancers	NH-A	brain
49	chr3:98496200-98497600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr3:98496200-98497800	Enhancers	NHDF-Ad	bronchial

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links