Variant report

Variant	rs6462866
Chromosome Location	chr7:38837536-38837537
allele	C/T
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	CTCF	chr7:38837420-38837570	Caco-2	colon:	n/a	n/a

Variant related genes	Relation type
VPS41	TF binding region

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs1012976	1.00[JPT][hapmap]
rs10224856	1.00[JPT][hapmap]
rs10225415	1.00[JPT][hapmap]
rs10239228	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10249968	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10254354	1.00[JPT][hapmap]
rs10270427	1.00[JPT][hapmap]
rs10951574	1.00[JPT][hapmap]
rs10951575	1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12701653	1.00[JPT][hapmap]
rs12701661	1.00[JPT][hapmap]
rs13224619	1.00[JPT][hapmap]
rs13230196	1.00[JPT][hapmap]
rs13235997	1.00[JPT][hapmap]
rs2040878	1.00[JPT][hapmap]
rs2107742	1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2189854	1.00[JPT][hapmap]
rs2214667	1.00[JPT][hapmap]
rs2214668	1.00[JPT][hapmap]
rs2215032	1.00[JPT][hapmap]
rs2245773	1.00[JPT][hapmap]
rs2286089	1.00[JPT][hapmap]
rs2286093	1.00[JPT][hapmap]
rs2286101	1.00[JPT][hapmap]
rs2286103	1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2286108	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2392599	1.00[JPT][hapmap]
rs2392610	1.00[JPT][hapmap]
rs37472	1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs37473	1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs37475	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs37477	1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs37478	1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs37479	1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4720302	1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4723780	1.00[JPT][hapmap]
rs4723781	1.00[JPT][hapmap]
rs4723784	1.00[JPT][hapmap]
rs4723786	1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4723787	1.00[JPT][hapmap]
rs4723802	1.00[JPT][hapmap]
rs6949958	1.00[JPT][hapmap]
rs6951429	1.00[JPT][hapmap]
rs6960945	1.00[JPT][hapmap]
rs6963090	1.00[JPT][hapmap]
rs6967384	1.00[JPT][hapmap]
rs6975410	1.00[JPT][hapmap]
rs6976302	1.00[JPT][hapmap]
rs6976579	1.00[JPT][hapmap]
rs6979423	1.00[JPT][hapmap]
rs757685	1.00[JPT][hapmap]
rs758087	1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7782140	1.00[JPT][hapmap]
rs7782277	1.00[JPT][hapmap]
rs7787423	1.00[JPT][hapmap]
rs7802510	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs976350	1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs976351	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1032637	chr7:38832627-38902723	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv887966	chr7:38835035-38933942	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:38793400-38861200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr7:38800200-38837600	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr7:38803200-38845400	Weak transcription	Colonic Mucosa	Colon
4	chr7:38803200-38846000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr7:38813800-38839600	Weak transcription	Right Ventricle	heart
6	chr7:38813800-38857400	Weak transcription	HSMM	muscle
7	chr7:38822400-38855200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr7:38825000-38837800	Weak transcription	Fetal Heart	heart
9	chr7:38829400-38837600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr7:38829400-38837600	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr7:38829400-38838200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr7:38829400-38839000	Weak transcription	Gastric	stomach
13	chr7:38829400-38841600	Weak transcription	Osteobl	bone
14	chr7:38829400-38846600	Weak transcription	Brain Anterior Caudate	brain
15	chr7:38829400-38846600	Weak transcription	Brain Substantia Nigra	brain
16	chr7:38829400-38846800	Weak transcription	Brain Cingulate Gyrus	brain
17	chr7:38829400-38854600	Weak transcription	Left Ventricle	heart
18	chr7:38829400-38855200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr7:38829400-38855600	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr7:38829400-38856400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr7:38829400-38864400	Weak transcription	Thymus	Thymus
22	chr7:38829400-38864600	Weak transcription	NHLF	lung
23	chr7:38829600-38838200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr7:38829800-38838200	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr7:38831000-38838000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr7:38831000-38838200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr7:38831000-38871200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr7:38831400-38838800	Weak transcription	Fetal Muscle Trunk	muscle
29	chr7:38831600-38839000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr7:38831800-38838000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr7:38831800-38841600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr7:38831800-38846400	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr7:38831800-38854800	Weak transcription	Fetal Stomach	stomach
34	chr7:38831800-38856800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr7:38831800-38856800	Weak transcription	Pancreas	Pancrea
36	chr7:38831800-38857000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr7:38831800-38867800	Weak transcription	Fetal Thymus	thymus
38	chr7:38832000-38846400	Weak transcription	K562	blood
39	chr7:38832000-38855600	Weak transcription	Dnd41	blood
40	chr7:38832000-38857400	Weak transcription	Lung	lung
41	chr7:38832400-38840000	Weak transcription	Fetal Muscle Leg	muscle
42	chr7:38832400-38855200	Weak transcription	Fetal Intestine Small	intestine
43	chr7:38832800-38857000	Weak transcription	Esophagus	oesophagus
44	chr7:38833400-38846800	Weak transcription	Brain Angular Gyrus	brain
45	chr7:38833400-38857000	Weak transcription	Duodenum Mucosa	Duodenum
46	chr7:38833400-38859400	Weak transcription	Spleen	Spleen
47	chr7:38833600-38857000	Weak transcription	Aorta	Aorta
48	chr7:38833600-38857200	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr7:38834400-38847200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr7:38834400-38863400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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