Variant report

Variant	rs1317628
Chromosome Location	chr15:43066569-43066570
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 73 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10220713	0.89[CHB][hapmap];0.89[JPT][hapmap];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10220718	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10220726	1.00[GIH][hapmap];1.00[EUR][1000 genomes]
rs10220875	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10438302	0.89[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs11070381	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[ASN][1000 genomes]
rs11070384	1.00[EUR][1000 genomes]
rs11504666	1.00[EUR][1000 genomes]
rs12324135	0.81[JPT][hapmap]
rs13379871	1.00[EUR][1000 genomes]
rs13380157	1.00[EUR][1000 genomes]
rs13380212	1.00[EUR][1000 genomes]
rs13380301	0.89[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.80[AFR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16956991	1.00[EUR][1000 genomes]
rs16957002	1.00[EUR][1000 genomes]
rs16957043	0.81[JPT][hapmap]
rs16957052	1.00[MEX][hapmap]
rs16957125	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16957138	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16957164	1.00[EUR][1000 genomes]
rs16957178	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs16957185	1.00[EUR][1000 genomes]
rs16957187	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16957201	1.00[EUR][1000 genomes]
rs16957224	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs16957292	1.00[EUR][1000 genomes]
rs16973395	1.00[EUR][1000 genomes]
rs1877137	1.00[EUR][1000 genomes]
rs1877138	1.00[EUR][1000 genomes]
rs1915243	0.90[JPT][hapmap]
rs2054388	1.00[EUR][1000 genomes]
rs28535059	1.00[EUR][1000 genomes]
rs34348991	1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs34436896	1.00[EUR][1000 genomes]
rs35584827	1.00[EUR][1000 genomes]
rs56894749	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57880396	1.00[EUR][1000 genomes]
rs58423426	1.00[AMR][1000 genomes]
rs58506324	0.84[ASN][1000 genomes]
rs58754188	0.85[ASN][1000 genomes]
rs58756153	0.85[ASN][1000 genomes]
rs59276064	1.00[EUR][1000 genomes]
rs60752181	0.96[ASN][1000 genomes]
rs60789298	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs60807675	1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs60832391	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60881935	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61433348	1.00[AMR][1000 genomes]
rs61682243	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6493058	1.00[MEX][hapmap]
rs7162040	1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[AMR][1000 genomes]
rs7163324	1.00[JPT][hapmap];1.00[MEX][hapmap]
rs7164041	1.00[EUR][1000 genomes]
rs7165249	1.00[ASW][hapmap];0.81[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.86[YRI][hapmap];0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7174661	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7177501	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs7181448	1.00[MEX][hapmap]
rs8023743	0.81[JPT][hapmap]
rs8027319	1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[AMR][1000 genomes]
rs8031111	1.00[EUR][1000 genomes]
rs8032994	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8039217	1.00[JPT][hapmap];1.00[MEX][hapmap]
rs8039346	1.00[JPT][hapmap]
rs8039438	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[ASN][1000 genomes]
rs8043143	0.81[JPT][hapmap]
rs9806161	1.00[EUR][1000 genomes]
rs9806313	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv528725	chr15:42755555-43104406	Weak transcription Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv427959	chr15:42931181-43207353	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv977054	chr15:43015821-43171355	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv1050128	chr15:43056145-43262736	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv542368	chr15:43056145-43262736	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv525461	chr15:43062548-43482127	Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	32 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	chr15:43029800-43071000	Weak transcription	Pancreas	Pancrea
2	chr15:43030000-43067200	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr15:43030000-43093600	Weak transcription	Colonic Mucosa	Colon
4	chr15:43038400-43067400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr15:43045400-43068000	Weak transcription	Fetal Heart	heart
6	chr15:43045600-43074400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr15:43051800-43069400	Weak transcription	Gastric	stomach
8	chr15:43051800-43070600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr15:43051800-43074600	Weak transcription	Right Ventricle	heart
10	chr15:43051800-43075000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr15:43051800-43083800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr15:43052000-43066600	Weak transcription	Ovary	ovary
13	chr15:43052000-43074600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr15:43053600-43112200	Weak transcription	Rectal Smooth Muscle	rectum
15	chr15:43054000-43074600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr15:43054000-43080200	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr15:43054600-43067200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr15:43054600-43068600	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr15:43054800-43067200	Weak transcription	Duodenum Mucosa	Duodenum
20	chr15:43054800-43146000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr15:43055200-43066600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr15:43055600-43066800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr15:43056800-43067200	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr15:43056800-43068200	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr15:43056800-43116800	Weak transcription	HepG2	liver
26	chr15:43057600-43107000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr15:43060800-43122200	Weak transcription	GM12878-XiMat	blood
28	chr15:43061000-43067400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr15:43061200-43074600	Weak transcription	HSMMtube	muscle
30	chr15:43062200-43067200	Weak transcription	Osteobl	bone
31	chr15:43062200-43069600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr15:43062600-43066800	Weak transcription	Primary neutrophils fromperipheralblood	blood
33	chr15:43062600-43070200	Strong transcription	Primary T cells from cord blood	blood
34	chr15:43062600-43087800	Weak transcription	K562	blood
35	chr15:43062800-43066600	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr15:43062800-43070200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr15:43062800-43075200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
38	chr15:43062800-43088600	Weak transcription	NHDF-Ad	bronchial
39	chr15:43063000-43083200	Weak transcription	Fetal Intestine Small	intestine
40	chr15:43063000-43093000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr15:43063200-43074600	Weak transcription	Hela-S3	cervix
42	chr15:43063400-43070000	Strong transcription	Monocytes-CD14+_RO01746	blood
43	chr15:43063400-43093600	Weak transcription	Esophagus	oesophagus
44	chr15:43063400-43136200	Weak transcription	Psoas Muscle	Psoas
45	chr15:43063600-43069400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr15:43063600-43069600	Strong transcription	Primary B cells from cord blood	blood
47	chr15:43063800-43066600	Genic enhancers	Skeletal Muscle Female	skeletal muscle
48	chr15:43063800-43069600	Strong transcription	Primary B cells from peripheral blood	blood
49	chr15:43063800-43070000	Strong transcription	Primary monocytes fromperipheralblood	blood
50	chr15:43064000-43068000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood

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