Variant report

Variant	rs1398937
Chromosome Location	chr4:89958997-89958998
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:89958290..89961976-chr4:89962319..89966068,4	K562	blood:
2	chr4:89958647..89961976-chr4:89962746..89966068,3	K562	blood:

Extended variants
information (count: 96 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs10001420	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10028121	0.86[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes]
rs10033435	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10033476	0.93[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10433881	0.89[ASN][1000 genomes]
rs11734924	0.89[CEU][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1246630	0.80[ASN][1000 genomes]
rs1246633	0.80[ASN][1000 genomes]
rs12645173	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs12647095	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12649875	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1272570	0.80[ASN][1000 genomes]
rs13105546	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13106968	0.80[ASN][1000 genomes]
rs13133608	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13138927	0.85[ASN][1000 genomes]
rs1355836	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1355837	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1398938	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1398939	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1398941	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1398943	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1513811	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1513812	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1513823	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1533288	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1533289	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1533294	0.82[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1708659	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1708671	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1708672	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1708673	0.92[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1708683	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1795730	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1795735	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1795737	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1795740	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1828735	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1996139	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2056013	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2102650	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2125410	0.82[CHB][hapmap]
rs2446295	0.80[ASN][1000 genomes]
rs2464511	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2464521	0.80[ASN][1000 genomes]
rs2609254	0.82[CHB][hapmap];0.80[ASN][1000 genomes]
rs2609263	0.82[CHB][hapmap];0.80[ASN][1000 genomes]
rs2609266	1.00[CEU][hapmap]
rs2609274	0.82[CHB][hapmap]
rs2670618	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2670619	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2670620	0.92[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2670627	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2670628	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2704580	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2704585	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];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2704592	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2704593	0.82[CHB][hapmap];0.80[ASN][1000 genomes]
rs28559811	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28658282	0.81[AMR][1000 genomes]
rs2869965	0.82[CHB][hapmap];0.80[ASN][1000 genomes]
rs2869989	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28718401	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28869547	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2904264	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4325981	0.85[ASN][1000 genomes]
rs4693219	0.85[AMR][1000 genomes]
rs4693984	0.83[AMR][1000 genomes]
rs4693987	0.85[ASN][1000 genomes]
rs59698155	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6532100	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6532113	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6823241	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6826482	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6834297	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6843986	0.82[ASN][1000 genomes]
rs6845264	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6846010	0.89[ASN][1000 genomes]
rs7657630	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7673427	0.80[ASN][1000 genomes]
rs7697878	0.80[ASN][1000 genomes]
rs8180333	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9307063	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs938265	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs938267	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs973680	0.80[ASN][1000 genomes]
rs993358	0.80[ASN][1000 genomes]
rs9999793	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9999873	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv470051	chr4:89644931-90643144	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv1009354	chr4:89725914-89985155	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv1007025	chr4:89837734-90098046	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv537176	chr4:89837734-90098046	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv461577	chr4:89904124-89986326	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
6	nsv594807	chr4:89904124-89986326	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
7	nsv1002448	chr4:89933385-90128133	Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:89937200-89975600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr4:89940400-89959000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr4:89940400-89961000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr4:89944200-89978000	Weak transcription	Pancreas	Pancrea
5	chr4:89945600-89963000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr4:89946200-89972800	Weak transcription	A549	lung
7	chr4:89956000-89959200	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
8	chr4:89956000-89959200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr4:89956600-89959400	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr4:89957400-89959000	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
11	chr4:89957400-89959000	ZNF genes & repeats	Fetal Intestine Small	intestine
12	chr4:89957600-89959000	ZNF genes & repeats	Primary hematopoietic stem cells	blood
13	chr4:89957600-89959000	ZNF genes & repeats	Fetal Muscle Leg	muscle
14	chr4:89957800-89959200	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
15	chr4:89957800-89959200	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
16	chr4:89957800-89959400	ZNF genes & repeats	Fetal Stomach	stomach
17	chr4:89958000-89959000	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
18	chr4:89958000-89972200	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr4:89958200-89959200	Weak transcription	Fetal Intestine Large	intestine
20	chr4:89958200-89974400	Weak transcription	Aorta	Aorta
21	chr4:89958400-89959400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr4:89958400-89959400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr4:89958400-89961600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr4:89958400-89962000	Weak transcription	Lung	lung
25	chr4:89958400-89965600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr4:89958400-89970200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr4:89958400-89971400	Weak transcription	Ovary	ovary
28	chr4:89958800-89959000	Enhancers	Skeletal Muscle Female	skeletal muscle
29	chr4:89958800-89960600	Weak transcription	Fetal Lung	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links