Variant report

Variant	rs28594159
Chromosome Location	chr9:116296813-116296814
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:116292161..116294607-chr9:116294873..116297808,2	K562	blood:
2	chr9:116295222..116298307-chr9:116341614..116344019,3	MCF-7	breast:
3	chr9:116294683..116297585-chr9:116300975..116302682,2	K562	blood:
4	chr9:116036981..116038602-chr9:116296351..116298357,2	MCF-7	breast:
5	chr9:116294716..116297353-chr9:116298669..116300217,2	K562	blood:

Variant related genes	Relation type
ENSG00000138835	Chromatin interaction
ENSG00000176386	Chromatin interaction
ENSG00000136875	Chromatin interaction

Extended variants
information (count: 172 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:167)

rs_ID	r²[population]
rs10116799	0.87[EUR][1000 genomes]
rs10125960	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10217341	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10481676	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10481677	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10981789	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10981803	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10981807	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10981808	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10981814	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10981816	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10981817	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10981819	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10981820	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10981821	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10981825	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10981826	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10981827	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10981828	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10981829	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10981831	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10981832	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12335716	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12336719	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12337340	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12338588	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12338697	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12338701	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12339493	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12339501	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12339617	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12340996	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12341332	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12341490	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12342508	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12342699	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12343129	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12343141	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12343940	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12344334	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12344578	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12345524	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12345968	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12346076	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12346087	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12346939	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12347895	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12348214	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12348239	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12349661	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12353541	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1890992	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2050865	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2050866	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28694002	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs28714985	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35270441	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35358414	0.80[EUR][1000 genomes]
rs35533905	0.80[EUR][1000 genomes]
rs3983381	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs41301525	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs41305473	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs41313331	0.87[EUR][1000 genomes]
rs4596719	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs55676913	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs55696921	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs55777057	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55805468	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs55931715	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55977108	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs56155263	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56276438	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56390346	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61749208	0.93[EUR][1000 genomes]
rs6478011	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6478016	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6478022	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6478023	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7018783	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7020623	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7021688	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7023661	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7024445	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7024612	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7024996	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7025170	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7025745	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7026568	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7026656	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7027024	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7027340	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7028327	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7029685	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7032311	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7037441	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7040031	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7041833	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7042290	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7042695	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7043140	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7043571	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7045347	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7046202	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7046427	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7047062	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7048208	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7048305	0.87[EUR][1000 genomes]
rs72760092	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72760093	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72760097	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72761903	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72761904	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72761966	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72761968	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72761972	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72761982	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72761985	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72761987	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72761988	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72761992	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72761994	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72761997	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72762002	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72763803	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72763804	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72763806	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72763816	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72763826	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72763827	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72763828	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72763831	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72763832	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72763842	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72763843	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72763846	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72763848	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72763849	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7848203	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7849841	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7851718	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7853373	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7853792	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7854197	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7855325	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7856515	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7857943	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7859047	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7860673	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7861248	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7863159	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7864645	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7865364	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7867353	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7870227	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7870451	0.86[EUR][1000 genomes]
rs7871186	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7872084	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7872192	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7872283	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs867375	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs884899	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9299215	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs944345	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs944346	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9657641	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9657658	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9657659	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]

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	nsv530949	chr9:115821128-116487796	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv893747	chr9:116214058-116386438	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv466508	chr9:116244982-116362738	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv615215	chr9:116244982-116362738	Weak transcription Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv526579	chr9:116244982-116391162	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:116264800-116298400	Weak transcription	Brain Germinal Matrix	brain
2	chr9:116269400-116303000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr9:116269600-116298400	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr9:116277200-116298600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr9:116277600-116298600	Weak transcription	Fetal Brain Female	brain
6	chr9:116287000-116311600	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
7	chr9:116287400-116306600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr9:116287400-116309200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr9:116287600-116302800	Strong transcription	Fetal Intestine Large	intestine
10	chr9:116288000-116299200	Weak transcription	Dnd41	blood
11	chr9:116288000-116308600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr9:116288800-116298000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr9:116288800-116308200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr9:116288800-116308200	Strong transcription	HUVEC	blood vessel
15	chr9:116289000-116306600	Strong transcription	Primary T helper cells fromperipheralblood	blood
16	chr9:116289000-116308400	Strong transcription	GM12878-XiMat	blood
17	chr9:116289600-116310000	Weak transcription	Fetal Kidney	kidney
18	chr9:116289800-116298200	Strong transcription	Fetal Intestine Small	intestine
19	chr9:116290000-116299000	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr9:116290200-116297800	Weak transcription	Brain Angular Gyrus	brain
21	chr9:116290600-116297800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr9:116290600-116298200	Weak transcription	Fetal Lung	lung
23	chr9:116290800-116297800	Strong transcription	Fetal Stomach	stomach
24	chr9:116290800-116299000	Strong transcription	Duodenum Mucosa	Duodenum
25	chr9:116291000-116298000	Weak transcription	Stomach Mucosa	stomach
26	chr9:116291000-116298600	Weak transcription	Esophagus	oesophagus
27	chr9:116291000-116310600	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr9:116291200-116297800	Strong transcription	Stomach Smooth Muscle	stomach
29	chr9:116291600-116298400	Weak transcription	Thymus	Thymus
30	chr9:116291600-116310400	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr9:116291800-116298200	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr9:116291800-116298400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr9:116291800-116298400	Strong transcription	Rectal Mucosa Donor 29	rectum
34	chr9:116291800-116299000	Weak transcription	Colon Smooth Muscle	Colon
35	chr9:116292000-116302800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
36	chr9:116292200-116298200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr9:116292200-116299800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
38	chr9:116292600-116298000	Weak transcription	Adipose Nuclei	Adipose
39	chr9:116292800-116298200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr9:116293000-116298400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr9:116293000-116299000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr9:116293200-116298200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr9:116293400-116298200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr9:116293600-116298400	Weak transcription	Psoas Muscle	Psoas
45	chr9:116293600-116303600	Weak transcription	Hela-S3	cervix
46	chr9:116293800-116298400	Weak transcription	Aorta	Aorta
47	chr9:116294000-116297400	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr9:116294000-116297800	Weak transcription	Brain Anterior Caudate	brain
49	chr9:116294400-116297400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr9:116294600-116297400	Weak transcription	Skeletal Muscle Female	skeletal muscle

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