Variant report

Variant	rs9355580
Chromosome Location	chr6:166853513-166853514
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	chr6:166851912..166853592-chr6:166854792..166857095,2	K562	blood:

Extended variants
information (count: 21 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10806850	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10806851	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10806852	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12153873	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12191994	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2281052	0.83[CEU][hapmap]
rs2294330	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4710049	0.86[EUR][1000 genomes]
rs4710050	0.86[EUR][1000 genomes]
rs4710051	0.86[CEU][hapmap];0.84[TSI][hapmap];0.86[EUR][1000 genomes]
rs6910121	0.90[CEU][hapmap];0.89[CHB][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6915132	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6932660	0.90[CEU][hapmap];0.89[CHB][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73033724	0.88[EUR][1000 genomes]
rs7739961	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7741232	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9295346	0.86[EUR][1000 genomes]
rs9355581	0.90[CEU][hapmap];0.89[CHB][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3490076	chr6:166727901-167306743	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases
2	esv3490077	chr6:166727901-167306743	Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases
3	nsv886937	chr6:166830696-166922813	Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9355580	UNC93A	cis	parietal	SCAN
rs9355580	PHF10	cis	cerebellum	SCAN
rs9355580	DACT2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:166808200-166911800	Weak transcription	Psoas Muscle	Psoas
2	chr6:166824000-166901400	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr6:166825200-166875800	Weak transcription	Colonic Mucosa	Colon
4	chr6:166827000-166873400	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr6:166827600-166867200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr6:166830000-166866600	Weak transcription	Fetal Intestine Large	intestine
7	chr6:166833200-166864400	Weak transcription	Fetal Kidney	kidney
8	chr6:166833200-166879000	Weak transcription	NH-A	brain
9	chr6:166833400-166854800	Weak transcription	Primary B cells from cord blood	blood
10	chr6:166833400-166879000	Weak transcription	HSMM	muscle
11	chr6:166833600-166859600	Weak transcription	HMEC	breast
12	chr6:166834000-166866400	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr6:166834200-166863800	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr6:166834200-166879400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr6:166834600-166862000	Weak transcription	NHDF-Ad	bronchial
16	chr6:166838000-166856000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr6:166838200-166860400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr6:166843000-166865200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr6:166844200-166860400	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr6:166844200-166865200	Weak transcription	Rectal Smooth Muscle	rectum
21	chr6:166845800-166860000	Weak transcription	Colon Smooth Muscle	Colon
22	chr6:166845800-166860200	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr6:166845800-166862000	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr6:166845800-166863400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr6:166846000-166859200	Weak transcription	Osteobl	bone
26	chr6:166846000-166860600	Weak transcription	Liver	Liver
27	chr6:166846000-166861000	Weak transcription	HSMMtube	muscle
28	chr6:166846000-166861800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr6:166846000-166862200	Weak transcription	Fetal Intestine Small	intestine
30	chr6:166846000-166863200	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr6:166846000-166881000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr6:166846200-166857000	Weak transcription	Stomach Smooth Muscle	stomach
33	chr6:166846200-166858000	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr6:166846200-166859400	Weak transcription	Duodenum Mucosa	Duodenum
35	chr6:166846200-166860400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr6:166847000-166855400	Weak transcription	Right Ventricle	heart
37	chr6:166847000-166855800	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr6:166847000-166858200	Weak transcription	NHLF	lung
39	chr6:166847000-166858600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr6:166847000-166858800	Weak transcription	Ovary	ovary
41	chr6:166847000-166859200	Weak transcription	Aorta	Aorta
42	chr6:166847800-166856400	Enhancers	Primary hematopoietic stem cells	blood
43	chr6:166847800-166859400	Enhancers	Fetal Thymus	thymus
44	chr6:166848800-166865200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr6:166849400-166861000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr6:166850200-166859400	Weak transcription	Esophagus	oesophagus
47	chr6:166850200-166862000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr6:166850200-166863400	Weak transcription	Stomach Mucosa	stomach
49	chr6:166850200-166865200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr6:166850200-166870000	Weak transcription	Right Atrium	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links