Variant report

Variant	rs4897241
Chromosome Location	chr6:128385998-128385999
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	NFIC	chr6:128385552-128386100	HepG2	liver:	n/a	n/a
2	FOXA1	chr6:128385208-128386106	HepG2	liver:	n/a	n/a
3	SP1	chr6:128385575-128386067	HepG2	liver:	n/a	n/a
4	FOXA1	chr6:128385256-128386200	HepG2	liver:	n/a	n/a
5	HDAC2	chr6:128385506-128386094	HepG2	liver:	n/a	chr6:128385952-128385966
6	TEAD4	chr6:128385502-128386099	HepG2	liver:	n/a	n/a
7	FOXA1	chr6:128385704-128386028	HepG2	liver:	n/a	n/a
8	HNF4A	chr6:128385546-128386082	HepG2	liver:	n/a	chr6:128385830-128385845 chr6:128385832-128385844 chr6:128385831-128385846 chr6:128385831-128385846 chr6:128385831-128385846
9	EP300	chr6:128385538-128386084	HepG2	liver:	n/a	chr6:128385945-128385959
10	ARID3A	chr6:128383944-128386015	HepG2	liver:	n/a	chr6:128384820-128384836

Variant related genes	Relation type
PTPRK	TF binding region

Extended variants
information (count: 90 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10046118	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10046119	0.90[TSI][hapmap];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10046162	0.85[CHD][hapmap];0.89[ASN][1000 genomes]
rs10499136	0.89[ASN][1000 genomes]
rs11962156	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11962619	0.92[ASN][1000 genomes]
rs11963140	0.92[ASN][1000 genomes]
rs11967205	0.80[ASN][1000 genomes]
rs11967507	0.92[ASN][1000 genomes]
rs13217988	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17055223	0.90[TSI][hapmap]
rs17055231	0.83[CEU][hapmap];0.82[EUR][1000 genomes]
rs17055235	0.92[ASN][1000 genomes]
rs1883810	0.83[CEU][hapmap];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2326672	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28874136	0.89[ASN][1000 genomes]
rs35335036	0.81[EUR][1000 genomes]
rs4265047	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4327718	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4336462	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4339480	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4345415	0.83[AMR][1000 genomes]
rs4421216	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4475344	0.83[CEU][hapmap];0.90[TSI][hapmap];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4496822	0.86[ASN][1000 genomes]
rs4498384	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4598101	0.89[CEU][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4895828	0.89[ASN][1000 genomes]
rs4895829	0.89[CEU][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4897239	0.89[CEU][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4897240	0.89[CEU][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4897242	0.89[CEU][hapmap];0.85[CHD][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4897243	0.89[CEU][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs58544367	0.89[ASN][1000 genomes]
rs58766015	0.92[ASN][1000 genomes]
rs60702670	0.92[ASN][1000 genomes]
rs6569520	0.83[CEU][hapmap];0.82[EUR][1000 genomes]
rs6569521	0.88[CEU][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6569522	0.89[CEU][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6569523	0.89[CEU][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6912749	0.85[CHD][hapmap];0.85[YRI][hapmap];0.97[ASN][1000 genomes]
rs6913095	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6913595	0.83[EUR][1000 genomes]
rs6928445	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6928496	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6928512	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6938574	0.89[CEU][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs71565676	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7341312	0.80[ASN][1000 genomes]
rs73582696	0.92[ASN][1000 genomes]
rs73773990	0.80[ASN][1000 genomes]
rs73773992	0.80[ASN][1000 genomes]
rs7752113	1.00[ASN][1000 genomes]
rs7756639	0.83[EUR][1000 genomes]
rs7757761	0.89[CEU][hapmap];0.85[CHD][hapmap];0.90[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7758689	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7769691	0.89[CEU][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7774703	0.89[CEU][hapmap];0.88[EUR][1000 genomes]
rs9321106	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9321107	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9321108	0.89[CEU][hapmap];0.84[EUR][1000 genomes]
rs9321109	0.89[CEU][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9321110	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9375546	0.89[CEU][hapmap];0.85[CHD][hapmap];0.90[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9388616	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9402016	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9482856	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9482858	0.83[CEU][hapmap];0.90[TSI][hapmap];0.80[EUR][1000 genomes]
rs9482859	0.90[TSI][hapmap];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9482860	0.83[CEU][hapmap];0.90[TSI][hapmap];0.82[EUR][1000 genomes]
rs9482861	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9482862	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9482863	0.83[CEU][hapmap];0.82[EUR][1000 genomes]
rs9482864	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9482865	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9482866	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9482867	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9482868	0.90[TSI][hapmap];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9482869	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9482871	0.89[CEU][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9482872	0.89[CEU][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9491904	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9491905	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9491906	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9491909	0.89[ASN][1000 genomes]
rs970363	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs970364	0.83[CEU][hapmap];0.82[EUR][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:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:128289000-128431000	Weak transcription	Psoas Muscle	Psoas
2	chr6:128311600-128387200	Weak transcription	NH-A	brain
3	chr6:128320800-128388200	Weak transcription	NHEK	skin
4	chr6:128326600-128388200	Weak transcription	HMEC	breast
5	chr6:128342600-128388600	Weak transcription	Fetal Brain Female	brain
6	chr6:128347000-128405200	Weak transcription	Lung	lung
7	chr6:128350000-128401000	Weak transcription	Small Intestine	intestine
8	chr6:128353200-128388400	Weak transcription	NHLF	lung
9	chr6:128361200-128388000	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr6:128367600-128398000	Weak transcription	HUVEC	blood vessel
11	chr6:128368400-128388000	Weak transcription	Fetal Muscle Leg	muscle
12	chr6:128369800-128388000	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr6:128370000-128388000	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr6:128370000-128412600	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr6:128370800-128388000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr6:128372400-128412200	Weak transcription	Placenta	Placenta
17	chr6:128373400-128388000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr6:128373600-128388400	Weak transcription	Fetal Brain Male	brain
19	chr6:128373800-128388000	Weak transcription	Thymus	Thymus
20	chr6:128374600-128419400	Weak transcription	Esophagus	oesophagus
21	chr6:128375000-128387400	Weak transcription	Ovary	ovary
22	chr6:128375000-128388400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr6:128375000-128419400	Weak transcription	Gastric	stomach
24	chr6:128375000-128433800	Weak transcription	Aorta	Aorta
25	chr6:128375400-128387800	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr6:128375600-128413000	Weak transcription	Colonic Mucosa	Colon
27	chr6:128377400-128388200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr6:128377600-128388400	Weak transcription	Adipose Nuclei	Adipose
29	chr6:128377800-128403400	Weak transcription	Fetal Kidney	kidney
30	chr6:128378000-128390200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr6:128378800-128388000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr6:128379000-128387400	Weak transcription	Fetal Stomach	stomach
33	chr6:128379000-128388000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr6:128379000-128432800	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr6:128379400-128386600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr6:128379400-128388000	Weak transcription	HSMMtube	muscle
37	chr6:128379400-128388600	Weak transcription	Left Ventricle	heart
38	chr6:128379400-128390400	Weak transcription	NHDF-Ad	bronchial
39	chr6:128379400-128396600	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr6:128379400-128412200	Weak transcription	Stomach Smooth Muscle	stomach
41	chr6:128379600-128386400	Weak transcription	Duodenum Mucosa	Duodenum
42	chr6:128379600-128390000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr6:128379800-128388000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr6:128379800-128389200	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr6:128380400-128388200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr6:128381000-128388200	Weak transcription	Fetal Muscle Trunk	muscle
47	chr6:128381600-128387200	Weak transcription	HSMM	muscle
48	chr6:128381800-128389200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr6:128382600-128387000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr6:128383000-128387600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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