Variant report

Variant	rs4972511
Chromosome Location	chr2:173372751-173372752
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:173372610..173374163-chr2:173375837..173378337,2	K562	blood:

Variant related genes	Relation type
ENSG00000225205	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10497383	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10497384	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1076596	1.00[ASW][hapmap];0.82[MEX][hapmap];0.82[YRI][hapmap]
rs11883720	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11887938	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11892037	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11896937	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[LWK][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11897024	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11898822	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12464480	1.00[ASW][hapmap]
rs12469788	0.81[CEU][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap]
rs1344272	0.93[CEU][hapmap]
rs1574258	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17286988	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17676243	1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs17676773	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17677404	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17727678	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17727732	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17739735	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17739946	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2178475	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2272498	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2293649	0.93[CEU][hapmap];0.81[TSI][hapmap]
rs36002642	0.86[ASN][1000 genomes]
rs3792255	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3792256	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3828342	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4074913	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4405727	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4619573	0.93[CEU][hapmap];1.00[YRI][hapmap]
rs4972510	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4972832	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4972836	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4972837	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55802347	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59300838	0.81[EUR][1000 genomes]
rs6433359	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6433360	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6715294	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6717877	0.82[CEU][hapmap];1.00[CHD][hapmap];0.86[MEX][hapmap]
rs6728123	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6728419	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6731691	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6746138	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6755605	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72892573	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72892577	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72892596	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72892601	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72894305	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72894375	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72894389	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72894396	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72894400	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72896105	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7564591	0.93[CEU][hapmap];0.90[TSI][hapmap]
rs7564654	0.93[CEU][hapmap];0.84[TSI][hapmap]
rs7566921	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7582972	0.93[CEU][hapmap];1.00[YRI][hapmap]
rs7594889	1.00[CHD][hapmap]
rs7609465	0.93[CEU][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533927	chr2:173161637-173796894	Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4972511	HOXD4	cis	cerebellum	SCAN
rs4972511	DCAF17	cis	cerebellum	SCAN

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:173330600-173373200	Strong transcription	NHEK	skin
2	chr2:173330600-173373400	Strong transcription	HUES48 Cell Line	embryonic stem cell
3	chr2:173330600-173373400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr2:173330600-173373600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr2:173330600-173374200	Weak transcription	Stomach Mucosa	stomach
6	chr2:173331000-173373200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr2:173331000-173373400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
8	chr2:173331000-173373800	Strong transcription	HMEC	breast
9	chr2:173347800-173376200	Weak transcription	Fetal Heart	heart
10	chr2:173352000-173374200	Weak transcription	Fetal Lung	lung
11	chr2:173356400-173379200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr2:173356600-173375400	Weak transcription	Brain Cingulate Gyrus	brain
13	chr2:173356800-173374600	Weak transcription	Fetal Kidney	kidney
14	chr2:173356800-173376000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr2:173356800-173376200	Weak transcription	Brain Substantia Nigra	brain
16	chr2:173357000-173373000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr2:173357000-173376000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr2:173357000-173376000	Weak transcription	Aorta	Aorta
19	chr2:173357200-173376600	Weak transcription	Right Ventricle	heart
20	chr2:173357600-173376200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr2:173358000-173376200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr2:173361000-173375600	Weak transcription	Spleen	Spleen
23	chr2:173361200-173373600	Strong transcription	Duodenum Mucosa	Duodenum
24	chr2:173361200-173375200	Weak transcription	GM12878-XiMat	blood
25	chr2:173361800-173373400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr2:173362800-173372800	Strong transcription	Primary T cells fromperipheralblood	blood
27	chr2:173365600-173373000	Weak transcription	Fetal Intestine Small	intestine
28	chr2:173366200-173374400	Strong transcription	HSMM	muscle
29	chr2:173367400-173376000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr2:173367600-173374400	Weak transcription	Colonic Mucosa	Colon
31	chr2:173368600-173374400	Strong transcription	HSMMtube	muscle
32	chr2:173369400-173374200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr2:173369600-173373000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr2:173369600-173373400	Weak transcription	Fetal Muscle Trunk	muscle
35	chr2:173369600-173374200	Weak transcription	Rectal Smooth Muscle	rectum
36	chr2:173369600-173374800	Weak transcription	HepG2	liver
37	chr2:173369600-173375000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr2:173369600-173375400	Weak transcription	Left Ventricle	heart
39	chr2:173369600-173375600	Weak transcription	Liver	Liver
40	chr2:173369600-173376000	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr2:173369600-173376000	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr2:173369600-173376000	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr2:173369600-173376000	Weak transcription	Esophagus	oesophagus
44	chr2:173369600-173376000	Weak transcription	HUVEC	blood vessel
45	chr2:173369800-173373000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr2:173369800-173374400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
47	chr2:173369800-173375600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr2:173369800-173375600	Weak transcription	Adipose Nuclei	Adipose
49	chr2:173369800-173376600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr2:173370000-173375000	Weak transcription	Primary T helper naive cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links