Variant report

Variant	rs259683
Chromosome Location	chr6:37874714-37874715
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:37874214..37875957-chr6:37876729..37879670,2	K562	blood:
2	chr6:37873838..37876151-chr6:37878592..37881455,2	K562	blood:
3	chr6:37873063..37875947-chr6:37943285..37945175,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AL353597.1-10	chr6:37872575-37875797	NONHSAT112287

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs11756656	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1212636	0.95[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap]
rs12211975	1.00[CEU][hapmap];0.95[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.89[EUR][1000 genomes]
rs174105	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs187741	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1885325	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1979759	0.89[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2055205	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2180514	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2201646	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[ASN][1000 genomes]
rs2395687	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs259672	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs259674	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs259675	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs259676	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs259677	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs259678	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs259682	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs259685	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs259687	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs259688	0.92[ASN][1000 genomes]
rs259693	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs259694	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs259714	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs259717	0.91[CHB][hapmap];0.85[JPT][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs259721	0.95[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap]
rs259722	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs259723	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3792706	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4142102	1.00[CEU][hapmap];0.95[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.88[EUR][1000 genomes]
rs4711522	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4711524	0.88[ASN][1000 genomes]
rs4714118	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4714123	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6458030	0.94[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6458036	0.92[ASN][1000 genomes]
rs6458040	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs67133782	0.88[EUR][1000 genomes]
rs67479083	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6912097	0.85[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs6915506	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs6917668	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6920185	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6926280	0.90[CHB][hapmap];0.83[JPT][hapmap]
rs6930859	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs6934617	1.00[CEU][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7765798	1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.86[ASN][1000 genomes]
rs9349053	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs9369029	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[ASN][1000 genomes]
rs9369033	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs9394469	0.81[AFR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9394471	0.86[ASN][1000 genomes]
rs9462374	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[ASN][1000 genomes]
rs9462380	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9470714	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9470723	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9470724	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9470725	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9470762	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9647620	0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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

No data

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:37850600-37890400	Weak transcription	Primary B cells from cord blood	blood
2	chr6:37851000-37884600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr6:37857600-37886000	Weak transcription	Esophagus	oesophagus
4	chr6:37857600-37895400	Weak transcription	Pancreas	Pancrea
5	chr6:37858000-37877600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr6:37862000-37877000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr6:37862400-37877200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr6:37862400-37884000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr6:37862600-37882000	Weak transcription	Fetal Intestine Small	intestine
10	chr6:37862800-37879000	Weak transcription	GM12878-XiMat	blood
11	chr6:37864600-37880800	Weak transcription	NHDF-Ad	bronchial
12	chr6:37865600-37879600	Weak transcription	Thymus	Thymus
13	chr6:37866000-37885600	Weak transcription	Hela-S3	cervix
14	chr6:37869400-37877000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr6:37870200-37877200	Weak transcription	Left Ventricle	heart
16	chr6:37871000-37874800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr6:37871400-37879400	Weak transcription	K562	blood
18	chr6:37872000-37887600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr6:37872000-37888200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr6:37872000-37890400	Weak transcription	Small Intestine	intestine
21	chr6:37872200-37883000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr6:37872200-37884000	Weak transcription	Adipose Nuclei	Adipose
23	chr6:37872200-37884600	Weak transcription	Fetal Kidney	kidney
24	chr6:37872400-37883000	Weak transcription	Brain Substantia Nigra	brain
25	chr6:37872600-37877200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr6:37872600-37877200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr6:37872600-37879600	Weak transcription	Psoas Muscle	Psoas
28	chr6:37872600-37885200	Weak transcription	HepG2	liver
29	chr6:37872600-37896400	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr6:37872800-37878400	Weak transcription	Fetal Heart	heart
31	chr6:37872800-37880600	Weak transcription	HMEC	breast
32	chr6:37872800-37880800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr6:37873000-37874800	Enhancers	Primary T helper cells fromperipheralblood	blood
34	chr6:37873000-37882600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr6:37873200-37878400	Weak transcription	Colon Smooth Muscle	Colon
36	chr6:37873200-37887400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr6:37873400-37877200	Weak transcription	Liver	Liver
38	chr6:37873400-37929200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr6:37873600-37875200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
40	chr6:37873800-37876600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
41	chr6:37874000-37878400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
42	chr6:37874000-37888400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr6:37874200-37875800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr6:37874200-37884600	Weak transcription	A549	lung
45	chr6:37874400-37874800	Weak transcription	Primary T helper cells PMA-I stimulated	--
46	chr6:37874400-37874800	Weak transcription	NH-A	brain
47	chr6:37874400-37875400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
48	chr6:37874400-37876200	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr6:37874400-37876400	Weak transcription	Primary T cells from cord blood	blood
50	chr6:37874400-37877200	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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