Variant report

Variant	rs2842517
Chromosome Location	chr6:37920953-37920954
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	chr6:37919246..37922240-chr6:37953708..37956298,2	K562	blood:
2	chr6:37920868..37922667-chr6:37923260..37925049,2	K562	blood:

Extended variants
information (count: 73 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10456096	0.89[CEU][hapmap];0.88[CHB][hapmap];0.83[AMR][1000 genomes]
rs10456097	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10485029	0.87[GIH][hapmap]
rs10947713	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1187421	0.82[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap]
rs1187422	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1187423	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12190570	0.89[CHB][hapmap]
rs12192182	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12194618	0.83[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs12198907	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12200258	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12204352	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs12206818	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12211248	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12211981	0.83[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12213151	0.81[EUR][1000 genomes]
rs12213835	0.91[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12214375	0.92[CEU][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap]
rs13210701	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13214465	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13220131	0.88[EUR][1000 genomes]
rs16890277	0.81[ASN][1000 genomes]
rs16890344	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap]
rs171831	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1812599	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2055206	0.80[CEU][hapmap]
rs2132597	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs259673	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs259679	0.89[CHB][hapmap]
rs259684	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs259686	0.83[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs259689	0.83[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs259690	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs259691	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs259695	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs259713	0.83[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs259715	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs259716	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs259718	0.89[CHB][hapmap]
rs2645102	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs2645107	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2645113	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2645116	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2645117	0.89[CHB][hapmap];1.00[CHD][hapmap]
rs2645120	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2645124	0.86[CHB][hapmap]
rs2645127	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2645128	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2645131	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.82[EUR][1000 genomes]
rs2645134	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs2645137	0.83[EUR][1000 genomes]
rs2842500	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2842527	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2842529	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2842531	0.83[LWK][hapmap];0.91[YRI][hapmap]
rs34871463	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35823566	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56098839	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6458029	0.96[CEU][hapmap];0.88[CHB][hapmap];0.84[YRI][hapmap]
rs7747130	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9296232	0.83[ASW][hapmap];0.96[CEU][hapmap];0.88[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs9394460	0.96[CEU][hapmap];0.88[CHB][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap]
rs9647619	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs966705	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][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	nsv1028825	chr6:37495154-38278320	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers 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
2	nsv1024016	chr6:37567651-37981590	Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1017051	chr6:37789341-38084719	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv538203	chr6:37789341-38084719	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1018711	chr6:37813397-37981590	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv1020625	chr6:37833591-38155622	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
7	nsv1021991	chr6:37893949-38738720	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
8	nsv602956	chr6:37909084-37986489	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2842517	SLC26A8	cis	cerebellum	SCAN
rs2842517	KCNK17	cis	parietal	SCAN
rs2842517	TAF11	cis	cerebellum	SCAN

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:37873400-37929200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr6:37880200-37930000	Weak transcription	Thymus	Thymus
3	chr6:37887600-37933200	Weak transcription	NHDF-Ad	bronchial
4	chr6:37892600-37928800	Weak transcription	Primary T cells fromperipheralblood	blood
5	chr6:37896800-37929000	Weak transcription	Esophagus	oesophagus
6	chr6:37904800-37933400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr6:37905800-37924000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr6:37907000-37921200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr6:37907000-37926600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr6:37910000-37922600	Weak transcription	Right Ventricle	heart
11	chr6:37911000-37933200	Weak transcription	NHEK	skin
12	chr6:37911400-37922600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr6:37911600-37928600	Weak transcription	Lung	lung
14	chr6:37911600-37935400	Weak transcription	Primary B cells from cord blood	blood
15	chr6:37911600-37936200	Weak transcription	Primary hematopoietic stem cells	blood
16	chr6:37912800-37922600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr6:37913400-37922600	Weak transcription	Aorta	Aorta
18	chr6:37913400-37922600	Weak transcription	Pancreas	Pancrea
19	chr6:37913400-37922600	Weak transcription	Right Atrium	heart
20	chr6:37914400-37923200	Weak transcription	Brain Anterior Caudate	brain
21	chr6:37914600-37921200	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr6:37914600-37923000	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr6:37915000-37923400	Weak transcription	Brain Substantia Nigra	brain
24	chr6:37915800-37921200	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr6:37916600-37923400	Weak transcription	Colon Smooth Muscle	Colon
26	chr6:37916800-37922600	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr6:37917000-37928800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr6:37917800-37922600	Weak transcription	Ovary	ovary
29	chr6:37917800-37928600	Weak transcription	Fetal Intestine Small	intestine
30	chr6:37918200-37926800	Weak transcription	Gastric	stomach
31	chr6:37918400-37924000	Weak transcription	Spleen	Spleen
32	chr6:37919600-37921000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr6:37919600-37921000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
34	chr6:37919600-37924000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr6:37919800-37921600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
36	chr6:37920000-37921400	Enhancers	Liver	Liver
37	chr6:37920000-37923200	Weak transcription	Primary T helper cells fromperipheralblood	blood
38	chr6:37920000-37933600	Weak transcription	Rectal Smooth Muscle	rectum
39	chr6:37920400-37921000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
40	chr6:37920400-37921400	Enhancers	Left Ventricle	heart
41	chr6:37920400-37921400	Enhancers	Psoas Muscle	Psoas
42	chr6:37920400-37921600	Enhancers	Small Intestine	intestine
43	chr6:37920600-37921000	Weak transcription	Stomach Mucosa	stomach
44	chr6:37920600-37922000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
45	chr6:37920600-37922600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr6:37920600-37922600	Weak transcription	Primary B cells from peripheral blood	blood
47	chr6:37920600-37922800	Weak transcription	Adipose Nuclei	Adipose
48	chr6:37920600-37923400	Weak transcription	Brain Hippocampus Middle	brain
49	chr6:37920600-37924600	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr6:37920600-37928000	Weak transcription	Primary T cells from cord blood	blood

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