Variant report

Variant	rs9496948
Chromosome Location	chr6:144702116-144702117
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs12660531	1.00[GIH][hapmap]
rs12662904	0.90[ASN][1000 genomes]
rs12663172	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs12663605	1.00[CHB][hapmap];0.80[CHD][hapmap];1.00[GIH][hapmap];0.85[ASN][1000 genomes]
rs12664421	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12665269	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17073598	1.00[GIH][hapmap]
rs17073629	1.00[GIH][hapmap]
rs4538732	0.80[YRI][hapmap]
rs58104509	0.93[EUR][1000 genomes]
rs58108287	0.93[EUR][1000 genomes]
rs59862970	0.93[EUR][1000 genomes]
rs60234245	0.90[ASN][1000 genomes]
rs6570623	0.93[EUR][1000 genomes]
rs6570625	0.86[AFR][1000 genomes]
rs6570627	0.81[YRI][hapmap]
rs6903993	0.93[AFR][1000 genomes]
rs6916795	1.00[GIH][hapmap]
rs6917034	1.00[CHB][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6936691	0.85[LWK][hapmap]
rs73594936	0.97[AFR][1000 genomes]
rs73594937	0.97[AFR][1000 genomes]
rs73594958	0.93[EUR][1000 genomes]
rs73594960	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73594967	0.93[EUR][1000 genomes]
rs73780544	0.97[AFR][1000 genomes]
rs7743190	1.00[YRI][hapmap];0.97[AFR][1000 genomes]
rs7745285	0.93[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs7745998	1.00[GIH][hapmap]
rs7751351	0.89[YRI][hapmap]
rs7761280	1.00[YRI][hapmap];0.97[AFR][1000 genomes]
rs7763097	0.85[CEU][hapmap]
rs7765364	1.00[CEU][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs7770411	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9321969	1.00[GIH][hapmap]
rs9496944	0.81[ASW][hapmap]
rs9496949	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9496950	0.93[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs9496954	0.81[ASW][hapmap];0.85[LWK][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	nsv830832	chr6:144572378-144759023	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	esv2422260	chr6:144574591-144731630	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv1031253	chr6:144599055-144883013	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv538461	chr6:144599055-144883013	Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:144683800-144704600	Weak transcription	Aorta	Aorta
2	chr6:144690800-144712800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr6:144691600-144713800	Weak transcription	Thymus	Thymus
4	chr6:144692400-144702200	Weak transcription	Monocytes-CD14+_RO01746	blood
5	chr6:144697000-144714800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr6:144697200-144732600	Weak transcription	Gastric	stomach
7	chr6:144699000-144702200	Weak transcription	Fetal Thymus	thymus
8	chr6:144699000-144708600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr6:144699400-144704400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr6:144699800-144704400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr6:144700000-144709800	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr6:144700600-144702200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr6:144700600-144702400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr6:144700600-144707000	Weak transcription	Lung	lung
15	chr6:144700600-144708800	Weak transcription	Adipose Nuclei	Adipose
16	chr6:144700600-144719200	Weak transcription	Ovary	ovary
17	chr6:144700800-144703800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
18	chr6:144700800-144704200	Weak transcription	Left Ventricle	heart
19	chr6:144700800-144704200	Weak transcription	Small Intestine	intestine
20	chr6:144700800-144705400	Weak transcription	Pancreas	Pancrea
21	chr6:144700800-144705400	Weak transcription	Psoas Muscle	Psoas
22	chr6:144700800-144707200	Weak transcription	Right Atrium	heart
23	chr6:144700800-144707200	Weak transcription	HUVEC	blood vessel
24	chr6:144700800-144712200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr6:144700800-144712200	Weak transcription	Right Ventricle	heart
26	chr6:144700800-144716000	Weak transcription	NHLF	lung
27	chr6:144700800-144719000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr6:144700800-144719000	Weak transcription	Esophagus	oesophagus
29	chr6:144700800-144719000	Weak transcription	Spleen	Spleen
30	chr6:144701000-144702200	Weak transcription	Primary T cells fromperipheralblood	blood
31	chr6:144701000-144708600	Weak transcription	Stomach Mucosa	stomach
32	chr6:144701200-144702200	Weak transcription	HepG2	liver
33	chr6:144701200-144703800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr6:144701200-144711200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr6:144701600-144702200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
36	chr6:144701800-144702200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr6:144701800-144702400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr6:144701800-144702400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr6:144701800-144703200	ZNF genes & repeats	Primary T cells from cord blood	blood
40	chr6:144701800-144703600	ZNF genes & repeats	Primary B cells from cord blood	blood
41	chr6:144701800-144703600	ZNF genes & repeats	Primary B cells from peripheral blood	blood
42	chr6:144702000-144702800	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
43	chr6:144702000-144703200	Weak transcription	Primary T helper cells PMA-I stimulated	--
44	chr6:144702000-144704000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr6:144702000-144705400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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