Variant report

Variant	rs388597
Chromosome Location	chr6:5124190-5124191
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:5120935..5125341-chr6:5126554..5131441,5	K562	blood:
2	chr6:5122792..5124780-chr6:5175533..5177529,2	K562	blood:

Extended variants
information (count: 69 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs175596	0.86[CHB][hapmap]
rs200844	0.82[AMR][1000 genomes]
rs200859	0.86[CHB][hapmap]
rs200860	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs200862	0.86[CHB][hapmap]
rs200866	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.86[GIH][hapmap];0.91[TSI][hapmap];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs200867	0.86[CHB][hapmap]
rs200868	0.86[CHB][hapmap]
rs200869	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs200870	0.86[CHB][hapmap]
rs364857	0.83[ASN][1000 genomes]
rs373696	0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs374117	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs379508	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs379511	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs381472	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs392847	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs393055	0.87[ASN][1000 genomes]
rs393300	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs393332	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs393628	0.82[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs394252	0.88[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs399120	0.86[CHB][hapmap]
rs411483	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs411893	0.81[ASN][1000 genomes]
rs414986	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs417629	0.93[ASN][1000 genomes]
rs424006	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.87[CHD][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs434706	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs438934	0.88[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs439911	1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs441463	0.88[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs441482	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs445229	0.81[ASN][1000 genomes]
rs445342	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs452908	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs453331	1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs456209	1.00[JPT][hapmap]
rs458108	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.91[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs458283	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs458743	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs460416	0.88[CHD][hapmap]
rs461465	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs462327	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs465453	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs465481	1.00[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs466285	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs591481	0.88[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs606033	0.85[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs620360	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs661578	0.83[ASN][1000 genomes]
rs667543	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs9405257	0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023527	chr6:4729592-5387176	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv462622	chr6:4904380-5172009	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv600871	chr6:4904380-5172009	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv600872	chr6:4975313-5342190	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	nsv1031837	chr6:4996667-5418726	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
6	nsv1017380	chr6:5007870-5152551	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
7	nsv1017373	chr6:5066785-5128943	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv538112	chr6:5066785-5128943	Enhancers Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv1034681	chr6:5070351-5387176	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
10	nsv538113	chr6:5070351-5387176	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
11	nsv1018152	chr6:5077025-5387176	Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
12	nsv600873	chr6:5089278-5400658	Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
13	nsv1017821	chr6:5114609-5213200	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA	5 gene(s)	inside rSNPs	diseases
14	nsv538114	chr6:5114609-5213200	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA	5 gene(s)	inside rSNPs	diseases
15	nsv981298	chr6:5118857-5126001	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
16	nsv5179	chr6:5121824-5167027	Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region miRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs388597	POMZP3	trans	lymphoblastoid	seeQTL

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:5099000-5130000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr6:5101800-5132200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr6:5103200-5132800	Weak transcription	Primary hematopoietic stem cells	blood
4	chr6:5105200-5131400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr6:5105800-5125600	Weak transcription	Ovary	ovary
6	chr6:5105800-5128200	Weak transcription	Primary B cells from cord blood	blood
7	chr6:5107800-5132000	Weak transcription	Pancreas	Pancrea
8	chr6:5109200-5130200	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr6:5112200-5128600	Weak transcription	Primary T cells from cord blood	blood
10	chr6:5112800-5124800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr6:5112800-5125400	Weak transcription	Right Atrium	heart
12	chr6:5112800-5132600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr6:5113000-5130400	Weak transcription	Gastric	stomach
14	chr6:5113200-5124800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr6:5113200-5130400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr6:5113400-5132400	Weak transcription	Stomach Smooth Muscle	stomach
17	chr6:5113800-5125400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr6:5116000-5129000	Weak transcription	Fetal Intestine Small	intestine
19	chr6:5117400-5125200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr6:5117600-5124600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr6:5119800-5125200	Weak transcription	A549	lung
22	chr6:5122200-5125200	Weak transcription	Adipose Nuclei	Adipose
23	chr6:5122400-5129000	Weak transcription	Fetal Stomach	stomach
24	chr6:5122800-5124600	Enhancers	Fetal Muscle Trunk	muscle
25	chr6:5122800-5125600	Enhancers	Fetal Muscle Leg	muscle
26	chr6:5123000-5126000	Weak transcription	Fetal Heart	heart
27	chr6:5123000-5128400	Weak transcription	Primary neutrophils fromperipheralblood	blood
28	chr6:5123200-5124800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr6:5123200-5124800	Weak transcription	Right Ventricle	heart
30	chr6:5123200-5124800	Weak transcription	Spleen	Spleen
31	chr6:5123200-5130400	Weak transcription	Left Ventricle	heart
32	chr6:5123400-5124800	Weak transcription	HepG2	liver
33	chr6:5123400-5125000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr6:5123400-5132200	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr6:5123600-5124800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr6:5123600-5129200	Weak transcription	Lung	lung
37	chr6:5123800-5124200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr6:5123800-5124600	Enhancers	Fetal Thymus	thymus
39	chr6:5124000-5124600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr6:5124000-5125000	Weak transcription	NHLF	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links