Variant report

Variant	rs2102397
Chromosome Location	chr4:48656326-48656327
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	POLR2A	chr4:48656287-48656653	H1-neurons	neurons:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:48652508..48655525-chr4:48656294..48658905,3	K562	blood:
2	chr4:48652921..48654969-chr4:48656237..48658200,2	K562	blood:
3	chr4:48635131..48636662-chr4:48655697..48657913,2	K562	blood:

Variant related genes	Relation type
FRYL	TF binding region
ENSG00000075539	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10049761	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap]
rs10938534	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap]
rs10938537	0.96[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.81[AMR][1000 genomes]
rs11727343	0.92[CEU][hapmap];0.82[CHB][hapmap];0.85[MEX][hapmap];0.88[TSI][hapmap]
rs11737677	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap]
rs11945562	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap]
rs12645501	0.87[CHB][hapmap];0.91[JPT][hapmap];0.92[YRI][hapmap]
rs13108474	0.81[AMR][1000 genomes]
rs13119041	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap]
rs13142540	0.89[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap]
rs13149083	0.88[CEU][hapmap];0.82[CHB][hapmap];0.85[MEX][hapmap]
rs1507865	0.87[CHB][hapmap];0.85[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.88[LWK][hapmap];0.85[TSI][hapmap];0.92[YRI][hapmap]
rs1517674	0.96[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap]
rs1554256	0.96[CEU][hapmap];0.87[CHB][hapmap];0.84[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap]
rs16861510	0.91[YRI][hapmap]
rs1712772	0.86[YRI][hapmap]
rs17575720	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap]
rs17656040	0.80[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap]
rs17656094	0.87[CHB][hapmap];0.91[JPT][hapmap];0.92[YRI][hapmap]
rs1876469	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap]
rs2176460	0.93[GIH][hapmap];0.91[JPT][hapmap];0.88[LWK][hapmap];0.85[TSI][hapmap];0.92[YRI][hapmap]
rs2354348	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap]
rs2354938	0.92[YRI][hapmap]
rs2572345	0.80[MEX][hapmap];0.92[YRI][hapmap]
rs2712156	0.92[YRI][hapmap]
rs28470767	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap]
rs3761729	0.82[CHB][hapmap];0.80[MEX][hapmap]
rs4536901	0.87[CHB][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.88[LWK][hapmap];0.82[TSI][hapmap];0.92[YRI][hapmap]
rs4694906	0.92[YRI][hapmap]
rs4695391	0.87[CHB][hapmap];0.83[CHD][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.88[LWK][hapmap];0.85[TSI][hapmap];0.92[YRI][hapmap]
rs4695407	0.86[CHB][hapmap]
rs6811148	0.87[CHB][hapmap];0.91[JPT][hapmap];0.92[YRI][hapmap]
rs6829716	0.87[CHB][hapmap];0.81[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap]
rs6830848	0.87[CHB][hapmap];0.91[JPT][hapmap];0.84[YRI][hapmap]
rs6836632	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap]
rs6843340	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes]
rs7654032	0.88[CEU][hapmap];0.82[CHB][hapmap]
rs7654770	0.87[CHB][hapmap];0.81[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap]
rs7657332	0.91[JPT][hapmap];0.84[TSI][hapmap];0.86[YRI][hapmap]
rs7657698	0.91[JPT][hapmap];0.92[YRI][hapmap]
rs7660206	1.00[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap]
rs7665209	0.80[MEX][hapmap]
rs7667288	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap]
rs7678379	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap]
rs7679210	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap]
rs7683398	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap]
rs7693461	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap]
rs7697522	0.91[JPT][hapmap];0.92[YRI][hapmap]
rs7697851	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap]
rs776584	0.87[CHB][hapmap];0.91[JPT][hapmap];0.92[YRI][hapmap]
rs776591	0.87[CHB][hapmap];0.91[JPT][hapmap];0.92[YRI][hapmap]
rs776602	0.92[YRI][hapmap]
rs796555	0.87[CHB][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.88[LWK][hapmap];0.85[TSI][hapmap];0.92[YRI][hapmap]
rs9291326	0.86[CHB][hapmap];0.81[MEX][hapmap]
rs937888	0.87[CHB][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.88[LWK][hapmap];0.85[TSI][hapmap];0.92[YRI][hapmap]
rs937889	0.87[CHB][hapmap];0.91[JPT][hapmap];0.84[YRI][hapmap]
rs952289	0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap]
rs992423	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap]
rs9997920	0.86[CHB][hapmap];0.81[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002674	chr4:48507608-49032909	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv537087	chr4:48507608-49032909	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv1010923	chr4:48575156-49083089	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv537088	chr4:48575156-49083089	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv1013762	chr4:48580484-49032909	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv537089	chr4:48580484-49032909	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv999203	chr4:48645887-48735512	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	esv1802666	chr4:48646594-48721327	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv1013914	chr4:48652784-48728934	Genic enhancers Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv537090	chr4:48652784-48728934	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2102397	OCIAD2	cis	lymphoblastoid	seeQTL
rs2102397	SLC10A4	cis	lung	GTEx
rs2102397	OCIAD2	cis	cerebellum	SCAN

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48621200-48729400	Weak transcription	Thymus	Thymus
2	chr4:48627200-48656400	Weak transcription	Fetal Intestine Small	intestine
3	chr4:48637600-48656400	Weak transcription	Primary T cells fromperipheralblood	blood
4	chr4:48637800-48664200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr4:48638000-48657200	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr4:48638000-48663000	Weak transcription	Primary monocytes fromperipheralblood	blood
7	chr4:48638000-48664600	Weak transcription	Primary B cells from peripheral blood	blood
8	chr4:48638400-48686200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr4:48638600-48666000	Weak transcription	Primary B cells from cord blood	blood
10	chr4:48645200-48679400	Weak transcription	Rectal Smooth Muscle	rectum
11	chr4:48645400-48656400	Weak transcription	Fetal Stomach	stomach
12	chr4:48645400-48656400	Weak transcription	Spleen	Spleen
13	chr4:48645400-48663400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr4:48645400-48664200	Weak transcription	Fetal Muscle Leg	muscle
15	chr4:48645600-48664200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr4:48648800-48669200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr4:48650600-48656400	Weak transcription	Esophagus	oesophagus
18	chr4:48653000-48666800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr4:48653000-48667600	Weak transcription	Duodenum Mucosa	Duodenum
20	chr4:48653200-48665800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr4:48653400-48656600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr4:48653400-48656600	Enhancers	NHEK	skin
23	chr4:48653400-48669200	Weak transcription	Gastric	stomach
24	chr4:48653600-48656400	Active TSS	Brain Anterior Caudate	brain
25	chr4:48653800-48656400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr4:48653800-48664600	Weak transcription	Primary hematopoietic stem cells	blood
27	chr4:48654000-48656800	Enhancers	HSMM	muscle
28	chr4:48654000-48657600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
29	chr4:48654200-48656400	Active TSS	Right Atrium	heart
30	chr4:48654400-48669600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr4:48654600-48657400	Enhancers	Primary T helper cells fromperipheralblood	blood
32	chr4:48654800-48657600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
33	chr4:48655000-48657600	Enhancers	Primary T helper cells PMA-I stimulated	--
34	chr4:48655000-48657600	Enhancers	Dnd41	blood
35	chr4:48655200-48657400	Enhancers	Primary T helper naive cells from peripheral blood	blood
36	chr4:48655400-48656600	Active TSS	Aorta	Aorta
37	chr4:48655400-48656600	Enhancers	Pancreas	Pancrea
38	chr4:48655400-48656600	Enhancers	Small Intestine	intestine
39	chr4:48655400-48656800	Enhancers	Fetal Heart	heart
40	chr4:48655400-48657200	Enhancers	NHDF-Ad	bronchial
41	chr4:48655400-48657400	Enhancers	Colon Smooth Muscle	Colon
42	chr4:48655400-48657600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
43	chr4:48655400-48657600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
44	chr4:48655400-48657600	Enhancers	HUVEC	blood vessel
45	chr4:48655400-48659200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr4:48655600-48656400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr4:48655600-48656400	Active TSS	Brain Hippocampus Middle	brain
48	chr4:48655600-48656600	Enhancers	HUES6 Cell Line	embryonic stem cell
49	chr4:48655600-48656600	Enhancers	HUES64 Cell Line	embryonic stem cell
50	chr4:48655600-48656800	Enhancers	Fetal Adrenal Gland	Adrenal Gland

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links