Variant report

Variant	rs10046162
Chromosome Location	chr6:128388238-128388239
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TCF7L2	chr6:128388021-128388430	HEK293	kidney:	n/a	n/a
2	KAP1	chr6:128388006-128388466	U2OS	brain:	n/a	n/a
3	RAD21	chr6:128388214-128388239	IMR90	lung:	n/a	n/a
4	KAP1	chr6:128388004-128388557	HEK293	kidney:	n/a	n/a
5	FOXP2	chr6:128388112-128388416	SK-N-MC	brain:	n/a	n/a

Variant related genes	Relation type
PTPRK	TF binding region

Extended variants
information (count: 126 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:123)

rs_ID	r²[population]
rs10046118	0.81[ASN][1000 genomes]
rs10046119	0.82[CHD][hapmap];0.81[ASN][1000 genomes]
rs10485161	0.82[EUR][1000 genomes]
rs10485162	0.82[EUR][1000 genomes]
rs10499136	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10499138	0.82[EUR][1000 genomes]
rs11962156	0.81[ASN][1000 genomes]
rs11962619	0.81[ASN][1000 genomes]
rs11962916	0.82[EUR][1000 genomes]
rs11963140	0.81[ASN][1000 genomes]
rs11964585	1.00[MEX][hapmap]
rs11967205	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11967507	0.81[ASN][1000 genomes]
rs11968433	0.82[EUR][1000 genomes]
rs11970637	0.82[EUR][1000 genomes]
rs13217988	0.81[ASN][1000 genomes]
rs17053270	0.82[EUR][1000 genomes]
rs17055235	0.84[CHD][hapmap];0.81[ASN][1000 genomes]
rs17055267	0.81[YRI][hapmap]
rs17055290	0.82[EUR][1000 genomes]
rs17055300	0.82[EUR][1000 genomes]
rs17055360	0.82[EUR][1000 genomes]
rs17055365	0.82[EUR][1000 genomes]
rs17055403	0.82[EUR][1000 genomes]
rs17055412	0.82[EUR][1000 genomes]
rs17055415	0.82[EUR][1000 genomes]
rs17055421	0.82[EUR][1000 genomes]
rs17055443	0.82[EUR][1000 genomes]
rs17055445	0.82[EUR][1000 genomes]
rs17055461	0.82[EUR][1000 genomes]
rs17055488	0.82[EUR][1000 genomes]
rs17055499	0.82[EUR][1000 genomes]
rs17055501	0.82[EUR][1000 genomes]
rs17055507	0.82[EUR][1000 genomes]
rs1738273	0.82[EUR][1000 genomes]
rs1768358	0.82[EUR][1000 genomes]
rs1856497	0.82[EUR][1000 genomes]
rs1883810	1.00[CHB][hapmap]
rs2326672	0.83[ASN][1000 genomes]
rs28874136	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4131020	0.82[EUR][1000 genomes]
rs4265047	0.81[ASN][1000 genomes]
rs4327718	0.81[ASN][1000 genomes]
rs4339480	0.81[ASN][1000 genomes]
rs4421216	0.81[ASN][1000 genomes]
rs4475344	0.83[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4496822	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4498384	0.81[ASN][1000 genomes]
rs4895828	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4895832	0.82[EUR][1000 genomes]
rs4897241	0.85[CHD][hapmap];0.89[ASN][1000 genomes]
rs4897242	1.00[CHD][hapmap];0.89[ASN][1000 genomes]
rs4897244	0.82[EUR][1000 genomes]
rs4897245	0.82[EUR][1000 genomes]
rs4897246	0.82[EUR][1000 genomes]
rs4897247	0.82[EUR][1000 genomes]
rs4897248	0.82[EUR][1000 genomes]
rs4897249	0.82[EUR][1000 genomes]
rs4897250	0.82[EUR][1000 genomes]
rs55828045	0.82[EUR][1000 genomes]
rs56042959	0.82[EUR][1000 genomes]
rs56932458	0.82[EUR][1000 genomes]
rs57797601	0.82[EUR][1000 genomes]
rs58544367	0.83[ASN][1000 genomes]
rs58652879	0.82[EUR][1000 genomes]
rs58706847	0.82[EUR][1000 genomes]
rs58766015	0.81[ASN][1000 genomes]
rs60264538	0.82[EUR][1000 genomes]
rs60436012	0.82[EUR][1000 genomes]
rs60702670	0.81[ASN][1000 genomes]
rs61111040	0.82[EUR][1000 genomes]
rs6900798	0.82[EUR][1000 genomes]
rs6905735	0.82[EUR][1000 genomes]
rs6909380	0.82[EUR][1000 genomes]
rs6910587	0.82[EUR][1000 genomes]
rs6912749	1.00[CHD][hapmap];0.85[ASN][1000 genomes]
rs6913095	0.83[ASN][1000 genomes]
rs6918772	0.82[EUR][1000 genomes]
rs6928445	0.81[ASN][1000 genomes]
rs6928496	0.81[ASN][1000 genomes]
rs6928512	0.81[ASN][1000 genomes]
rs6929394	0.82[EUR][1000 genomes]
rs6929623	0.82[EUR][1000 genomes]
rs6933133	0.82[EUR][1000 genomes]
rs6938199	0.82[EUR][1000 genomes]
rs71565676	0.83[ASN][1000 genomes]
rs7341312	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs73582696	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73588698	0.82[EUR][1000 genomes]
rs73590666	0.82[EUR][1000 genomes]
rs73592613	0.82[EUR][1000 genomes]
rs73592686	0.82[EUR][1000 genomes]
rs73773990	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73773992	0.91[ASN][1000 genomes]
rs7751187	0.82[EUR][1000 genomes]
rs7751946	0.90[YRI][hapmap];1.00[AMR][1000 genomes]
rs7752113	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7754637	0.82[EUR][1000 genomes]
rs7757761	1.00[CHD][hapmap];0.89[ASN][1000 genomes]
rs7758689	0.89[ASN][1000 genomes]
rs7768121	0.82[EUR][1000 genomes]
rs7772200	0.82[EUR][1000 genomes]
rs9321107	0.81[ASN][1000 genomes]
rs9321110	0.89[ASN][1000 genomes]
rs9375546	1.00[CHD][hapmap];0.89[ASN][1000 genomes]
rs9388616	0.81[ASN][1000 genomes]
rs9402016	0.89[ASN][1000 genomes]
rs9482856	0.91[ASN][1000 genomes]
rs9482859	0.84[CHD][hapmap];0.81[ASN][1000 genomes]
rs9482861	0.81[ASN][1000 genomes]
rs9482862	0.81[ASN][1000 genomes]
rs9482864	0.81[ASN][1000 genomes]
rs9482865	0.81[ASN][1000 genomes]
rs9482866	0.81[ASN][1000 genomes]
rs9482867	0.81[ASN][1000 genomes]
rs9482868	0.84[CHD][hapmap];0.81[ASN][1000 genomes]
rs9482869	0.81[ASN][1000 genomes]
rs9482872	0.89[ASN][1000 genomes]
rs9491904	0.81[ASN][1000 genomes]
rs9491905	0.81[ASN][1000 genomes]
rs9491906	0.81[ASN][1000 genomes]
rs9491909	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs970363	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1033443	chr6:128306654-128899203	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv538440	chr6:128306654-128899203	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv604643	chr6:128359362-128493991	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:128289000-128431000	Weak transcription	Psoas Muscle	Psoas
2	chr6:128342600-128388600	Weak transcription	Fetal Brain Female	brain
3	chr6:128347000-128405200	Weak transcription	Lung	lung
4	chr6:128350000-128401000	Weak transcription	Small Intestine	intestine
5	chr6:128353200-128388400	Weak transcription	NHLF	lung
6	chr6:128367600-128398000	Weak transcription	HUVEC	blood vessel
7	chr6:128370000-128412600	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr6:128372400-128412200	Weak transcription	Placenta	Placenta
9	chr6:128373600-128388400	Weak transcription	Fetal Brain Male	brain
10	chr6:128374600-128419400	Weak transcription	Esophagus	oesophagus
11	chr6:128375000-128388400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr6:128375000-128419400	Weak transcription	Gastric	stomach
13	chr6:128375000-128433800	Weak transcription	Aorta	Aorta
14	chr6:128375600-128413000	Weak transcription	Colonic Mucosa	Colon
15	chr6:128377600-128388400	Weak transcription	Adipose Nuclei	Adipose
16	chr6:128377800-128403400	Weak transcription	Fetal Kidney	kidney
17	chr6:128378000-128390200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr6:128379000-128432800	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr6:128379400-128388600	Weak transcription	Left Ventricle	heart
20	chr6:128379400-128390400	Weak transcription	NHDF-Ad	bronchial
21	chr6:128379400-128396600	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr6:128379400-128412200	Weak transcription	Stomach Smooth Muscle	stomach
23	chr6:128379600-128390000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr6:128379800-128389200	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr6:128381800-128389200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr6:128383000-128389400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr6:128384000-128389600	Strong transcription	Primary B cells from peripheral blood	blood
28	chr6:128384000-128396000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr6:128385000-128388600	Strong transcription	Primary B cells from cord blood	blood
30	chr6:128385000-128390800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr6:128385200-128388800	Enhancers	Brain Angular Gyrus	brain
32	chr6:128385400-128389000	Strong transcription	Fetal Thymus	thymus
33	chr6:128385600-128388400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr6:128385600-128389000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr6:128385800-128406400	Weak transcription	Primary T cells from cord blood	blood
36	chr6:128385800-128419400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr6:128386400-128389600	Strong transcription	Duodenum Mucosa	Duodenum
38	chr6:128386600-128388800	Enhancers	Right Atrium	heart
39	chr6:128387000-128389000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
40	chr6:128387000-128389600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr6:128387200-128389000	Strong transcription	HSMM	muscle
42	chr6:128387200-128389400	Strong transcription	NH-A	brain
43	chr6:128387200-128389600	Strong transcription	Liver	Liver
44	chr6:128387400-128388800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr6:128387400-128389000	Strong transcription	Pancreas	Pancrea
46	chr6:128387400-128389600	Strong transcription	Fetal Stomach	stomach
47	chr6:128387400-128389600	Strong transcription	Ovary	ovary
48	chr6:128387600-128389600	Strong transcription	Fetal Intestine Large	intestine
49	chr6:128387600-128389600	Strong transcription	HepG2	liver
50	chr6:128387600-128390200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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