Variant report

Variant	rs9396258
Chromosome Location	chr6:56959731-56959732
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:56959009..56963624-chr6:57035365..57039055,4	K562	blood:
2	chr6:56959009..56961254-chr6:57035519..57038371,2	K562	blood:
3	chr6:56957996..56959783-chr6:57181332..57183913,2	MCF-7	breast:
4	chr6:56954882..56956500-chr6:56957366..56960018,2	MCF-7	breast:
5	chr6:56951498..56953476-chr6:56957306..56959983,2	K562	blood:
6	chr6:56913257..56915032-chr6:56957847..56960567,2	K562	blood:
7	chr12:77457691..77459253-chr6:56958727..56961580,2	MCF-7	breast:
8	chr6:56958459..56961139-chr6:57008086..57010930,2	K562	blood:
9	chr6:56959161..56962012-chr6:57000090..57002565,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000146143	Chromatin interaction
ENSG00000226803	Chromatin interaction
ENSG00000112208	Chromatin interaction
ENSG00000112200	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs1002996	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1040461	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12175661	0.83[AMR][1000 genomes]
rs1556245	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16888316	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1993118	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2273919	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3757296	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4510664	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58705880	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61740375	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62415861	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62415862	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62415863	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62415864	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62415865	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62415878	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62415879	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62415880	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62415883	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62415884	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62415885	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62417430	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6459179	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6907653	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6932278	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72867038	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72867054	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72867059	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72867062	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7749960	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7766234	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7771328	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9296860	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9296861	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9349844	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9349845	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9357936	0.80[AMR][1000 genomes]
rs9357939	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9357940	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9357941	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9367706	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9367707	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9367709	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9367710	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9367711	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9367713	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9367714	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9370559	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9370561	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9370562	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9370563	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9370567	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9370568	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9382684	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9382685	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9382686	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9382691	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs9396254	0.80[AMR][1000 genomes]
rs9396255	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9396260	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9396261	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9396263	0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9464416	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9464418	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9464419	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9475768	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9475774	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9475778	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9475781	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9475782	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9475783	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9475788	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491933	chr6:56177722-57171010	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv934026	chr6:56382056-57184218	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv533050	chr6:56504480-57297586	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	nsv1021651	chr6:56569444-56966319	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv538228	chr6:56569444-56966319	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
6	esv3430228	chr6:56830972-57079281	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	nsv350038	chr6:56953752-56960124	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56954000-56966800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr6:56955200-56960200	Weak transcription	Fetal Muscle Trunk	muscle
3	chr6:56955200-56960200	Weak transcription	Left Ventricle	heart
4	chr6:56955200-56960600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr6:56955200-56961600	Weak transcription	Lung	lung
6	chr6:56955200-56961800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr6:56955200-56962200	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr6:56955200-56962800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr6:56955200-56963800	Weak transcription	Colonic Mucosa	Colon
10	chr6:56955200-56964200	Weak transcription	Psoas Muscle	Psoas
11	chr6:56955200-56964400	Weak transcription	Pancreas	Pancrea
12	chr6:56955200-56964400	Weak transcription	Spleen	Spleen
13	chr6:56955200-56965400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr6:56955200-56965600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr6:56955200-56965800	Weak transcription	Esophagus	oesophagus
16	chr6:56956200-56960200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
17	chr6:56956200-56960200	Enhancers	Primary T helper cells fromperipheralblood	blood
18	chr6:56956400-56960600	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr6:56956600-56960800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr6:56956600-56961600	Weak transcription	Fetal Muscle Leg	muscle
21	chr6:56956600-56965200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr6:56956600-56965600	Weak transcription	Gastric	stomach
23	chr6:56956800-56960000	Enhancers	Rectal Smooth Muscle	rectum
24	chr6:56956800-56963800	Weak transcription	Stomach Smooth Muscle	stomach
25	chr6:56957000-56960200	Weak transcription	Fetal Stomach	stomach
26	chr6:56957000-56960800	Enhancers	Colon Smooth Muscle	Colon
27	chr6:56957000-56962000	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr6:56957000-56962000	Weak transcription	HSMMtube	muscle
29	chr6:56957000-56963400	Weak transcription	Thymus	Thymus
30	chr6:56957000-56963800	Weak transcription	Primary neutrophils fromperipheralblood	blood
31	chr6:56957000-56964000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr6:56957000-56964400	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr6:56957000-56965200	Weak transcription	Small Intestine	intestine
34	chr6:56957000-56965400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr6:56957000-56965800	Weak transcription	Stomach Mucosa	stomach
36	chr6:56957200-56959800	Strong transcription	HUES64 Cell Line	embryonic stem cell
37	chr6:56957200-56960200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr6:56957200-56960200	Weak transcription	Fetal Intestine Small	intestine
39	chr6:56957200-56961400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr6:56957200-56962000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr6:56957200-56962000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr6:56957200-56962200	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr6:56957200-56963000	Weak transcription	Fetal Lung	lung
44	chr6:56957200-56963200	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr6:56957200-56963800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr6:56957400-56963000	Weak transcription	NHLF	lung
47	chr6:56957400-56963600	Weak transcription	Fetal Kidney	kidney
48	chr6:56957600-56960600	Strong transcription	HUES48 Cell Line	embryonic stem cell
49	chr6:56957600-56962200	Weak transcription	Primary hematopoietic stem cells	blood
50	chr6:56957600-56967600	Strong transcription	Primary hematopoietic stem cells short term culture	blood

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