Variant report

Variant	rs10499230
Chromosome Location	chr6:144860889-144860890
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:144860540..144863082-chr6:144868271..144870923,2	K562	blood:
2	chr6:144860787..144863095-chr6:144885052..144886553,2	K562	blood:

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10080939	0.90[EUR][1000 genomes]
rs10447422	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10457761	0.85[CHB][hapmap]
rs10457764	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11155359	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11155367	0.92[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap]
rs11155369	0.85[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap]
rs11756963	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12190718	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12192622	0.85[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12198720	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap]
rs12200263	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12202537	0.86[CEU][hapmap];0.95[GIH][hapmap];0.82[MEX][hapmap];0.94[TSI][hapmap]
rs12202539	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12204734	0.86[CEU][hapmap];0.85[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12205460	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12209699	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12209889	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17073869	0.87[EUR][1000 genomes]
rs17793570	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1918749	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28588721	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34810766	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4259269	0.92[CEU][hapmap];0.95[GIH][hapmap]
rs4460225	0.87[EUR][1000 genomes]
rs4544928	0.84[YRI][hapmap]
rs4584002	0.91[GIH][hapmap]
rs4615409	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4896724	0.90[GIH][hapmap]
rs55833104	0.86[ASN][1000 genomes]
rs56264877	0.87[EUR][1000 genomes]
rs60530618	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6570634	0.85[CHB][hapmap];0.93[GIH][hapmap]
rs6908911	0.90[GIH][hapmap]
rs6912724	0.85[CHB][hapmap];0.90[GIH][hapmap]
rs6917268	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6917519	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6923281	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6942069	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73600166	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73600170	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73603015	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7773603	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9321976	0.85[CHB][hapmap]
rs9321977	0.95[GIH][hapmap]
rs9496982	0.93[GIH][hapmap]
rs9497026	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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	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
2	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
3	nsv1015228	chr6:144780458-144989321	Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv538462	chr6:144780458-144989321	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:144803400-144869800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr6:144807400-144904000	Weak transcription	Brain Substantia Nigra	brain
3	chr6:144812400-144881000	Weak transcription	Stomach Mucosa	stomach
4	chr6:144812600-144869800	Weak transcription	Colon Smooth Muscle	Colon
5	chr6:144815200-144881000	Weak transcription	NHEK	skin
6	chr6:144816600-144881400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr6:144821200-144861000	Weak transcription	Rectal Smooth Muscle	rectum
8	chr6:144829800-144863800	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr6:144831400-144879000	Strong transcription	Primary B cells from cord blood	blood
10	chr6:144832400-144862200	Weak transcription	Small Intestine	intestine
11	chr6:144833800-144868200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr6:144837200-144880800	Weak transcription	Brain Angular Gyrus	brain
13	chr6:144844400-144861400	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr6:144844400-144870000	Weak transcription	Brain Hippocampus Middle	brain
15	chr6:144850000-144864200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr6:144850000-144864200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr6:144850200-144877400	Weak transcription	HMEC	breast
18	chr6:144850400-144864000	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr6:144850400-144864200	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr6:144850400-144865600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr6:144850400-144866000	Weak transcription	Hela-S3	cervix
22	chr6:144850400-144903200	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr6:144850400-144903200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr6:144850400-144904200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr6:144850600-144862200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr6:144850600-144863400	Weak transcription	Fetal Intestine Small	intestine
27	chr6:144850600-144863600	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr6:144850600-144865800	Weak transcription	NHLF	lung
29	chr6:144850600-144870800	Weak transcription	Right Ventricle	heart
30	chr6:144850600-144881600	Weak transcription	Brain Anterior Caudate	brain
31	chr6:144850800-144861000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr6:144850800-144863600	Weak transcription	Colonic Mucosa	Colon
33	chr6:144851600-144861600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr6:144852200-144862000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr6:144852400-144861000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr6:144852400-144861000	Weak transcription	Esophagus	oesophagus
37	chr6:144852400-144861000	Weak transcription	Thymus	Thymus
38	chr6:144852400-144861400	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr6:144852400-144862000	Weak transcription	Spleen	Spleen
40	chr6:144852400-144870600	Weak transcription	Aorta	Aorta
41	chr6:144853000-144861600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr6:144853600-144863400	Weak transcription	Lung	lung
43	chr6:144853600-144896400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr6:144853800-144863600	Weak transcription	Fetal Stomach	stomach
45	chr6:144854000-144863400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr6:144854400-144861000	Weak transcription	Ovary	ovary
47	chr6:144854400-144861600	Weak transcription	NHDF-Ad	bronchial
48	chr6:144854400-144862800	Weak transcription	Gastric	stomach
49	chr6:144854400-144864200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr6:144854400-144873400	Weak transcription	Pancreas	Pancrea

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