Variant report

Variant	rs9378968
Chromosome Location	chr6:5581224-5581225
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:5579091..5581648-chr6:5587396..5590119,2	K562	blood:

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11752390	0.86[GIH][hapmap]
rs4573125	0.93[CEU][hapmap];0.91[JPT][hapmap];0.91[YRI][hapmap]
rs55735025	0.81[AFR][1000 genomes]
rs6927274	0.97[EUR][1000 genomes]
rs7744150	0.81[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs7744285	0.96[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs7767977	0.82[GIH][hapmap];0.86[JPT][hapmap]
rs7768379	0.93[CEU][hapmap];0.91[JPT][hapmap];0.91[YRI][hapmap]
rs9378430	1.00[CEU][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap]
rs9378431	1.00[ASW][hapmap];0.80[CHD][hapmap];0.86[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];0.96[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs9378967	0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1019428	chr6:5216835-5627839	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv538118	chr6:5216835-5627839	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv916361	chr6:5315853-5695486	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv883420	chr6:5524393-5584422	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv5181	chr6:5536921-5581595	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv600887	chr6:5545046-5694713	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv1016905	chr6:5566364-5639167	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv981213	chr6:5578587-5582864	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9378968	SLC22A23	cis	parietal	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:5565200-5583200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr6:5574200-5583400	Weak transcription	NHDF-Ad	bronchial
3	chr6:5576200-5581400	Weak transcription	Primary B cells from cord blood	blood
4	chr6:5577400-5639800	Weak transcription	Fetal Intestine Small	intestine
5	chr6:5578200-5584200	Weak transcription	Fetal Lung	lung
6	chr6:5580600-5582000	Enhancers	Primary T helper cells PMA-I stimulated	--
7	chr6:5580800-5581600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr6:5580800-5581600	Enhancers	Primary T cells from cord blood	blood
9	chr6:5580800-5581800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
10	chr6:5580800-5581800	Enhancers	Fetal Muscle Leg	muscle
11	chr6:5580800-5582000	Enhancers	Primary B cells from peripheral blood	blood
12	chr6:5580800-5582000	Enhancers	Primary T cells fromperipheralblood	blood
13	chr6:5580800-5582200	Enhancers	Fetal Thymus	thymus
14	chr6:5580800-5582800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
15	chr6:5581000-5582000	Enhancers	Primary T helper naive cells from peripheral blood	blood
16	chr6:5581000-5582000	Enhancers	Dnd41	blood
17	chr6:5581000-5582600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr6:5581000-5614200	Weak transcription	Lung	lung
19	chr6:5581000-5640400	Weak transcription	Gastric	stomach
20	chr6:5581200-5581600	Enhancers	Muscle Satellite Cultured Cells	--
21	chr6:5581200-5581600	Enhancers	Brain Hippocampus Middle	brain
22	chr6:5581200-5581600	Enhancers	Fetal Muscle Trunk	muscle
23	chr6:5581200-5581600	Enhancers	Skeletal Muscle Female	skeletal muscle
24	chr6:5581200-5581600	Enhancers	HSMMtube	muscle
25	chr6:5581200-5581800	Enhancers	Primary T helper cells fromperipheralblood	blood
26	chr6:5581200-5582000	Enhancers	Thymus	Thymus
27	chr6:5581200-5582000	Flanking Active TSS	GM12878-XiMat	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links