Variant report

Variant	rs9398506
Chromosome Location	chr6:119667412-119667413
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:119648699..119654492-chr6:119662714..119668241,6	K562	blood:
2	chr6:119606943..119609052-chr6:119667352..119668942,2	K562	blood:
3	chr6:119469648..119470479-chr6:119666850..119667538,2	MCF-7	breast:
4	chr6:119649666..119652399-chr6:119665160..119668137,2	K562	blood:
5	chr6:119666514..119668057-chr6:120002574..120005085,2	MCF-7	breast:
6	chr6:119666964..119669354-chr6:119827597..119829582,2	K562	blood:
7	chr6:119658599..119660724-chr6:119666324..119670101,4	K562	blood:

Variant related genes	Relation type
ENSG00000111879	Chromatin interaction

Extended variants
information (count: 96 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs1005506	0.81[ASW][hapmap];1.00[JPT][hapmap]
rs10872174	0.81[ASN][1000 genomes]
rs11153815	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12526344	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12528127	0.82[AMR][1000 genomes]
rs12529667	1.00[CEU][hapmap];0.87[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12530171	1.00[CEU][hapmap];0.87[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1295374	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1295375	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1295380	1.00[CEU][hapmap];0.87[CHB][hapmap];0.92[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1295394	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1342313	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1418376	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1555684	0.93[CHB][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs171843	0.88[CEU][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs195047	0.89[ASN][1000 genomes]
rs195049	0.88[ASN][1000 genomes]
rs195050	0.84[AMR][1000 genomes]
rs195053	0.93[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs195054	0.88[CEU][hapmap];0.93[CHB][hapmap];0.87[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.92[TSI][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs195055	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs195057	0.88[CEU][hapmap];0.93[CHB][hapmap];0.90[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.85[TSI][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs195060	0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs195061	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs195065	0.94[ASN][1000 genomes]
rs195067	0.86[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs195068	0.83[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs195069	0.94[ASN][1000 genomes]
rs195070	0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs195072	0.92[ASN][1000 genomes]
rs195073	0.94[ASN][1000 genomes]
rs195074	0.94[ASN][1000 genomes]
rs195077	0.88[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs195082	0.94[ASN][1000 genomes]
rs195084	0.94[ASN][1000 genomes]
rs195086	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs195087	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs195093	0.88[ASN][1000 genomes]
rs2064161	0.83[AMR][1000 genomes]
rs2066350	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2142885	0.87[CHB][hapmap];0.81[JPT][hapmap]
rs2142891	0.81[ASN][1000 genomes]
rs2295203	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2299884	0.87[CHB][hapmap];0.81[JPT][hapmap]
rs28364655	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3778110	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs3798655	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3822998	0.81[ASN][1000 genomes]
rs4945636	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4945638	0.80[AMR][1000 genomes]
rs4946409	0.84[AFR][1000 genomes]
rs4946416	0.82[AMR][1000 genomes]
rs56095132	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6569059	0.81[ASW][hapmap]
rs6569060	0.86[CHB][hapmap]
rs6569061	0.86[CHB][hapmap]
rs6569062	0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs66524742	0.87[ASN][1000 genomes]
rs6900388	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6903155	0.84[ASN][1000 genomes]
rs6903680	1.00[CEU][hapmap];0.87[CHB][hapmap];0.93[JPT][hapmap];0.82[YRI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6924723	0.84[AFR][1000 genomes]
rs6925366	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6932066	0.88[ASN][1000 genomes]
rs6933961	0.93[CHB][hapmap];0.81[ASN][1000 genomes]
rs72952933	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72952941	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7765368	0.89[MEX][hapmap]
rs7775421	0.87[CHB][hapmap];0.80[JPT][hapmap]
rs885028	0.80[AMR][1000 genomes]
rs9320682	0.81[ASN][1000 genomes]
rs9320683	0.81[ASN][1000 genomes]
rs9320684	0.81[JPT][hapmap]
rs9372528	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9372531	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9372534	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9374784	0.88[AMR][1000 genomes]
rs9374785	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9374786	0.81[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.85[MKK][hapmap];0.92[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9374789	0.81[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.85[TSI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9374790	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9385071	0.89[AMR][1000 genomes]
rs9387645	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9387647	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9387650	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9398507	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9398508	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9398509	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9401136	0.92[AMR][1000 genomes]
rs9489650	0.88[ASN][1000 genomes]
rs980818	0.92[CHB][hapmap]
rs998194	0.87[CHB][hapmap]

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	nsv1025995	chr6:119407742-119709548	Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	esv3447598	chr6:119558591-120119384	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	esv3389526	chr6:119558598-120190087	ZNF genes & repeats Enhancers Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	esv1802628	chr6:119647135-119678881	Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:119625200-119668600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:119636200-119667800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr6:119641400-119668200	Weak transcription	Fetal Muscle Trunk	muscle
4	chr6:119645000-119668200	Weak transcription	Aorta	Aorta
5	chr6:119648200-119668000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr6:119648200-119668000	Weak transcription	Esophagus	oesophagus
7	chr6:119652200-119667600	Weak transcription	Thymus	Thymus
8	chr6:119652200-119667600	Weak transcription	NHLF	lung
9	chr6:119653200-119667600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr6:119653200-119667800	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr6:119657800-119667600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr6:119658800-119667800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr6:119660800-119667600	Weak transcription	Fetal Brain Male	brain
14	chr6:119661200-119668000	Weak transcription	Fetal Muscle Leg	muscle
15	chr6:119661400-119668000	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr6:119661600-119667800	Weak transcription	Primary T cells from cord blood	blood
17	chr6:119661600-119667800	Transcr. at gene 5' and 3'	HepG2	liver
18	chr6:119662200-119669200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr6:119662600-119667600	Weak transcription	Primary B cells from peripheral blood	blood
20	chr6:119662600-119667600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr6:119662600-119667600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr6:119662600-119667600	Weak transcription	Left Ventricle	heart
23	chr6:119662600-119668600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr6:119662800-119667600	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr6:119662800-119667600	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr6:119662800-119667600	Weak transcription	Brain Angular Gyrus	brain
27	chr6:119662800-119667800	Weak transcription	Fetal Thymus	thymus
28	chr6:119663600-119667600	Weak transcription	Stomach Mucosa	stomach
29	chr6:119664000-119667600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr6:119664000-119667600	Weak transcription	Monocytes-CD14+_RO01746	blood
31	chr6:119664000-119668200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr6:119664400-119667600	Enhancers	Fetal Heart	heart
33	chr6:119664400-119668600	Transcr. at gene 5' and 3'	K562	blood
34	chr6:119664800-119672400	Active TSS	Brain Anterior Caudate	brain
35	chr6:119665000-119668600	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
36	chr6:119665000-119669200	Weak transcription	Spleen	Spleen
37	chr6:119665200-119667600	Weak transcription	Fetal Lung	lung
38	chr6:119665200-119667800	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr6:119665200-119672800	Active TSS	Pancreatic Islets	Pancreatic Islet
40	chr6:119665600-119667600	Enhancers	Primary T helper cells PMA-I stimulated	--
41	chr6:119665600-119667800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
42	chr6:119665600-119668600	Enhancers	Primary T helper cells fromperipheralblood	blood
43	chr6:119665800-119667600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr6:119665800-119667600	Weak transcription	Colonic Mucosa	Colon
45	chr6:119665800-119667600	Weak transcription	Lung	lung
46	chr6:119665800-119667600	Weak transcription	Rectal Smooth Muscle	rectum
47	chr6:119665800-119668000	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells	blood
48	chr6:119665800-119668200	Weak transcription	Ovary	ovary
49	chr6:119666200-119672600	Active TSS	NHDF-Ad	bronchial
50	chr6:119666400-119667600	Weak transcription	Fetal Intestine Small	intestine

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