Variant report

Variant	rs17454834
Chromosome Location	chr6:88330964-88330965
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	chr6:88320993..88323406-chr6:88329947..88331786,2	K562	blood:
2	chr6:88326068..88328832-chr6:88329382..88333308,3	K562	blood:

Extended variants
information (count: 90 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs13193193	1.00[AFR][1000 genomes]
rs13193470	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13196538	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13196755	0.87[EUR][1000 genomes]
rs13198094	0.87[EUR][1000 genomes]
rs13198372	0.84[AMR][1000 genomes]
rs13200106	0.84[AMR][1000 genomes]
rs13203649	0.87[EUR][1000 genomes]
rs13203957	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13206536	0.87[EUR][1000 genomes]
rs13206957	0.87[EUR][1000 genomes]
rs13208201	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs13208550	0.84[AMR][1000 genomes]
rs13211833	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs13213285	0.87[EUR][1000 genomes]
rs13215013	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs13216482	1.00[AFR][1000 genomes]
rs13216727	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs13219631	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs17455002	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17504517	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs2307383	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2307389	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2307393	0.87[EUR][1000 genomes]
rs28381487	0.87[EUR][1000 genomes]
rs28381518	0.87[EUR][1000 genomes]
rs28381552	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28385591	0.87[EUR][1000 genomes]
rs34006571	0.84[AMR][1000 genomes]
rs34007246	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs34008333	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs34154420	0.87[EUR][1000 genomes]
rs34423353	0.87[EUR][1000 genomes]
rs34455158	0.87[EUR][1000 genomes]
rs34650015	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs34941612	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35056836	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs35058527	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35116392	0.84[AMR][1000 genomes]
rs35145047	0.87[EUR][1000 genomes]
rs35303040	0.80[AMR][1000 genomes]
rs35324020	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35326820	0.84[AMR][1000 genomes]
rs35363104	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs35440627	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs35465301	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs35494431	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35593940	0.84[AMR][1000 genomes]
rs35607770	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs35866706	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs35917348	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35925514	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35946241	0.87[EUR][1000 genomes]
rs35965137	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs35972482	0.84[AMR][1000 genomes]
rs36020402	0.87[EUR][1000 genomes]
rs36041712	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs36090981	0.87[EUR][1000 genomes]
rs3757369	0.80[AMR][1000 genomes]
rs3763176	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs4409162	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs55686846	1.00[AFR][1000 genomes]
rs55759644	0.87[EUR][1000 genomes]
rs55880748	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs56031077	0.87[EUR][1000 genomes]
rs57526195	0.87[EUR][1000 genomes]
rs60313720	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs61432898	1.00[AFR][1000 genomes]
rs62417674	0.84[AMR][1000 genomes]
rs62417675	0.84[AMR][1000 genomes]
rs62417676	0.84[AMR][1000 genomes]
rs62417692	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs62417693	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs62417698	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62417700	1.00[AFR][1000 genomes]
rs62417715	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62417720	0.87[EUR][1000 genomes]
rs62417727	0.87[EUR][1000 genomes]
rs62417753	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62417757	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs62419368	1.00[AFR][1000 genomes]
rs62419377	1.00[AFR][1000 genomes]
rs7749032	0.87[EUR][1000 genomes]
rs7750528	0.87[EUR][1000 genomes]
rs7759422	0.87[EUR][1000 genomes]
rs7771832	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1031961	chr6:88110401-88367006	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv1031460	chr6:88153079-88410050	Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv1026482	chr6:88164934-88409728	Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1027706	chr6:88168987-88409728	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:88300600-88391200	Weak transcription	Colonic Mucosa	Colon
2	chr6:88301000-88347200	Weak transcription	Small Intestine	intestine
3	chr6:88301200-88385000	Weak transcription	Colon Smooth Muscle	Colon
4	chr6:88301400-88338400	Weak transcription	NHLF	lung
5	chr6:88301400-88354400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr6:88301400-88354600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr6:88302000-88347400	Weak transcription	Brain Cingulate Gyrus	brain
8	chr6:88302000-88354400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr6:88302000-88354600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr6:88305000-88398800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr6:88308800-88369800	Weak transcription	Fetal Brain Male	brain
12	chr6:88311400-88334600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr6:88312200-88371200	Weak transcription	NHEK	skin
14	chr6:88312400-88380600	Weak transcription	Brain Substantia Nigra	brain
15	chr6:88313800-88338200	Weak transcription	NHDF-Ad	bronchial
16	chr6:88314000-88384800	Weak transcription	Hela-S3	cervix
17	chr6:88314200-88399200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr6:88314600-88385000	Weak transcription	Esophagus	oesophagus
19	chr6:88315400-88334600	Strong transcription	HUES48 Cell Line	embryonic stem cell
20	chr6:88316600-88381200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr6:88316600-88390000	Weak transcription	Pancreas	Pancrea
22	chr6:88316800-88337800	Weak transcription	GM12878-XiMat	blood
23	chr6:88319000-88333000	Weak transcription	HepG2	liver
24	chr6:88320400-88400800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr6:88321200-88348400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr6:88321600-88350000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr6:88322000-88346200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr6:88322000-88352800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr6:88322200-88334400	Strong transcription	HUES64 Cell Line	embryonic stem cell
30	chr6:88322600-88344800	Weak transcription	HMEC	breast
31	chr6:88322800-88331200	Weak transcription	HSMM	muscle
32	chr6:88322800-88338400	Weak transcription	Osteobl	bone
33	chr6:88322800-88344000	Weak transcription	Liver	Liver
34	chr6:88322800-88344800	Weak transcription	NH-A	brain
35	chr6:88322800-88382000	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr6:88323000-88332400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr6:88323000-88332800	Weak transcription	Brain Angular Gyrus	brain
38	chr6:88323000-88333000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr6:88323000-88342000	Weak transcription	K562	blood
40	chr6:88323000-88344600	Weak transcription	Brain Hippocampus Middle	brain
41	chr6:88323000-88344800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr6:88323000-88346200	Weak transcription	Fetal Kidney	kidney
43	chr6:88323000-88366400	Weak transcription	A549	lung
44	chr6:88324000-88331000	Weak transcription	H1 Cell Line	embryonic stem cell
45	chr6:88324000-88344000	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr6:88324000-88347400	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr6:88324000-88369800	Weak transcription	Rectal Smooth Muscle	rectum
48	chr6:88324000-88385000	Weak transcription	Gastric	stomach
49	chr6:88324200-88331200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr6:88324200-88333000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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