Variant report

Variant	rs2182659
Chromosome Location	chr6:33751767-33751768
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:33751578-33751915	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:33750065..33752378-chr6:33760799..33763522,2	MCF-7	breast:

Variant related genes	Relation type
LEMD2	TF binding region

Extended variants
information (count: 67 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10672	1.00[JPT][hapmap]
rs10755683	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs10947428	0.84[CEU][hapmap]
rs10947436	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10947446	0.94[CEU][hapmap];1.00[CHB][hapmap];0.84[AFR][1000 genomes]
rs11751943	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1318691	0.88[EUR][1000 genomes]
rs1536500	0.91[EUR][1000 genomes]
rs1536501	0.92[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1547668	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[MEX][hapmap];0.84[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1951930	0.83[AFR][1000 genomes]
rs1998949	0.83[CEU][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes]
rs2182658	0.85[ASW][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.88[EUR][1000 genomes]
rs2395401	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2395446	0.88[EUR][1000 genomes]
rs2395447	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2395448	0.89[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs2967	1.00[JPT][hapmap]
rs3957165	0.88[CEU][hapmap];1.00[CHB][hapmap]
rs4711350	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4713676	0.83[EUR][1000 genomes]
rs4713685	0.85[ASW][hapmap]
rs4713687	0.85[AFR][1000 genomes]
rs4713688	0.85[AFR][1000 genomes]
rs487835	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs498114	1.00[JPT][hapmap]
rs4996878	0.88[EUR][1000 genomes]
rs4996879	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs530614	0.92[ASW][hapmap];0.89[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.90[TSI][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs549652	0.88[GIH][hapmap];1.00[JPT][hapmap]
rs570749	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs597386	0.88[GIH][hapmap];1.00[JPT][hapmap]
rs602399	0.92[ASW][hapmap];0.89[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.80[MEX][hapmap];0.86[TSI][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs608971	1.00[JPT][hapmap]
rs623813	1.00[GIH][hapmap];1.00[JPT][hapmap]
rs652049	0.92[ASW][hapmap];0.89[CEU][hapmap];1.00[GIH][hapmap];0.88[LWK][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs654682	1.00[JPT][hapmap]
rs658087	0.88[GIH][hapmap];1.00[JPT][hapmap]
rs680608	0.94[ASN][1000 genomes]
rs684119	0.88[GIH][hapmap];1.00[JPT][hapmap]
rs688209	0.84[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs6913517	1.00[JPT][hapmap]
rs6915136	0.88[GIH][hapmap];1.00[JPT][hapmap]
rs6921772	0.88[EUR][1000 genomes]
rs7449707	0.82[EUR][1000 genomes]
rs751727	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs756138	0.96[YRI][hapmap];0.88[EUR][1000 genomes]
rs756139	0.85[ASW][hapmap];0.85[TSI][hapmap];0.96[YRI][hapmap];0.88[EUR][1000 genomes]
rs764753	1.00[JPT][hapmap]
rs7739273	0.95[YRI][hapmap];0.88[EUR][1000 genomes]
rs791904	0.80[AFR][1000 genomes];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9380379	0.86[EUR][1000 genomes]
rs942496	0.92[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[LWK][hapmap];0.81[YRI][hapmap];0.85[AFR][1000 genomes]
rs943463	0.89[CEU][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.88[EUR][1000 genomes]
rs943464	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap];0.85[YRI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs943465	0.86[EUR][1000 genomes]
rs943472	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs943473	0.88[EUR][1000 genomes]
rs943476	0.92[ASW][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.88[EUR][1000 genomes]
rs9461905	0.89[CEU][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs9461907	0.92[EUR][1000 genomes]
rs9469542	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv885772	chr6:33638180-33767727	Bivalent Enhancer Genic enhancers Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
2	nsv462897	chr6:33717770-33778964	Genic enhancers Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv602839	chr6:33717770-33778964	Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv462898	chr6:33723383-33768897	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
5	nsv602840	chr6:33723383-33768897	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2182659	C6orf125	cis	cerebellum	SCAN
rs2182659	RXRB	cis	Skin Sun Exposed Lower leg	GTEx
rs2182659	BAK1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33738600-33753200	Strong transcription	Thymus	Thymus
2	chr6:33739600-33752600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr6:33739600-33754000	Strong transcription	Primary neutrophils fromperipheralblood	blood
4	chr6:33739800-33752400	Strong transcription	Primary T helper cells PMA-I stimulated	--
5	chr6:33739800-33752600	Strong transcription	Primary T helper cells fromperipheralblood	blood
6	chr6:33739800-33753000	Strong transcription	Primary B cells from peripheral blood	blood
7	chr6:33739800-33753000	Strong transcription	Primary T cells from cord blood	blood
8	chr6:33739800-33753000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr6:33739800-33753600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
10	chr6:33740000-33752400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr6:33740000-33752600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr6:33740000-33752600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr6:33740000-33752800	Strong transcription	Dnd41	blood
14	chr6:33740000-33753000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr6:33740000-33753000	Strong transcription	HepG2	liver
16	chr6:33740000-33753200	Strong transcription	Primary hematopoietic stem cells	blood
17	chr6:33740000-33753600	Strong transcription	Primary monocytes fromperipheralblood	blood
18	chr6:33740000-33753600	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr6:33740200-33751800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr6:33740200-33752400	Strong transcription	Rectal Smooth Muscle	rectum
21	chr6:33740200-33752600	Strong transcription	Primary T helper naive cells from peripheral blood	blood
22	chr6:33740200-33753000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr6:33740200-33753400	Strong transcription	Rectal Mucosa Donor 31	rectum
24	chr6:33740200-33754000	Strong transcription	Primary B cells from cord blood	blood
25	chr6:33740400-33752600	Strong transcription	Colon Smooth Muscle	Colon
26	chr6:33740400-33752800	Strong transcription	Duodenum Smooth Muscle	Duodenum
27	chr6:33740400-33753200	Strong transcription	Aorta	Aorta
28	chr6:33740400-33753600	Strong transcription	Sigmoid Colon	Sigmoid Colon
29	chr6:33740600-33753000	Strong transcription	Liver	Liver
30	chr6:33740600-33753000	Strong transcription	Colonic Mucosa	Colon
31	chr6:33740600-33754200	Strong transcription	Fetal Intestine Large	intestine
32	chr6:33740600-33754200	Strong transcription	Fetal Intestine Small	intestine
33	chr6:33741000-33752600	Strong transcription	Duodenum Mucosa	Duodenum
34	chr6:33741000-33753000	Strong transcription	Rectal Mucosa Donor 29	rectum
35	chr6:33741000-33753200	Strong transcription	Fetal Brain Female	brain
36	chr6:33741000-33754000	Strong transcription	Fetal Thymus	thymus
37	chr6:33741400-33753000	Strong transcription	Fetal Lung	lung
38	chr6:33741400-33753000	Strong transcription	Ovary	ovary
39	chr6:33741400-33753200	Strong transcription	Fetal Stomach	stomach
40	chr6:33741800-33752600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr6:33741800-33752800	Strong transcription	Fetal Kidney	kidney
42	chr6:33742400-33752000	Strong transcription	Primary T killer memory cells from peripheral blood	blood
43	chr6:33742400-33752800	Strong transcription	Small Intestine	intestine
44	chr6:33743200-33753200	Strong transcription	GM12878-XiMat	blood
45	chr6:33744200-33754400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr6:33744600-33752000	Strong transcription	Brain Cingulate Gyrus	brain
47	chr6:33744600-33753000	Strong transcription	Brain Substantia Nigra	brain
48	chr6:33744800-33751800	Strong transcription	Brain Inferior Temporal Lobe	brain
49	chr6:33745000-33752800	Strong transcription	Brain Hippocampus Middle	brain
50	chr6:33746200-33752800	Strong transcription	Brain Germinal Matrix	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links