Variant report

Variant	rs17694112
Chromosome Location	chr4:87728676-87728677
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10012566	0.88[ASN][1000 genomes]
rs10015639	0.81[CEU][hapmap]
rs10050311	0.94[CEU][hapmap];0.84[CHB][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes]
rs1021101	0.82[GIH][hapmap]
rs1035191	0.85[JPT][hapmap]
rs10516778	0.87[GIH][hapmap];0.90[JPT][hapmap];0.84[TSI][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10516786	0.81[CEU][hapmap]
rs11561681	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11930396	0.90[CHB][hapmap];0.82[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.91[ASN][1000 genomes]
rs12171458	0.91[ASN][1000 genomes]
rs13113689	0.84[JPT][hapmap]
rs1420621	0.85[CHB][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap]
rs17012072	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17012170	0.85[CEU][hapmap]
rs17012200	0.81[CEU][hapmap]
rs17419627	0.82[GIH][hapmap]
rs17419929	0.82[GIH][hapmap]
rs17420607	0.88[CEU][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];0.88[TSI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17420966	0.86[CEU][hapmap];0.82[CHB][hapmap];0.87[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17454154	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17454662	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17751557	0.87[CEU][hapmap]
rs2006842	0.85[JPT][hapmap]
rs2054592	0.88[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2054593	0.85[JPT][hapmap]
rs2230600	1.00[ASW][hapmap];0.88[CEU][hapmap];0.95[GIH][hapmap];0.80[JPT][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];0.91[TSI][hapmap];0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2287147	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3775236	0.85[JPT][hapmap]
rs3775238	0.82[CEU][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3775239	0.85[JPT][hapmap]
rs4263359	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4693150	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4693152	0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs4693154	0.87[CEU][hapmap]
rs4693780	0.82[CEU][hapmap];0.84[CHB][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes]
rs4693784	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4693795	0.81[CEU][hapmap]
rs55670248	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6531941	0.81[CEU][hapmap]
rs67867077	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72665791	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72665795	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7658220	0.87[ASN][1000 genomes]
rs7688019	0.95[CHB][hapmap];0.84[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.87[ASN][1000 genomes]
rs9307026	0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs969734	0.88[CEU][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][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	nsv594787	chr4:87221827-87888667	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv830001	chr4:87585278-87748643	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	4 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	chr4:87635200-87737400	Weak transcription	Fetal Brain Male	brain
2	chr4:87639400-87739200	Weak transcription	A549	lung
3	chr4:87642400-87735800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr4:87661600-87737800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr4:87661800-87728800	Weak transcription	Pancreas	Pancrea
6	chr4:87689400-87738200	Weak transcription	Gastric	stomach
7	chr4:87690000-87738800	Weak transcription	Rectal Smooth Muscle	rectum
8	chr4:87690800-87736000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr4:87692800-87734200	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr4:87694400-87735600	Weak transcription	Stomach Smooth Muscle	stomach
11	chr4:87696800-87733600	Weak transcription	NHLF	lung
12	chr4:87698600-87738600	Weak transcription	Brain Angular Gyrus	brain
13	chr4:87712000-87736600	Weak transcription	Fetal Muscle Trunk	muscle
14	chr4:87712400-87728800	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr4:87712600-87733600	Weak transcription	Lung	lung
16	chr4:87712600-87735800	Weak transcription	Brain Germinal Matrix	brain
17	chr4:87712600-87737600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr4:87712600-87738400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr4:87712600-87751400	Weak transcription	Aorta	Aorta
20	chr4:87712800-87732000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr4:87712800-87736400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr4:87712800-87737000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr4:87712800-87739600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr4:87714400-87731800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr4:87715600-87732600	Weak transcription	Brain Substantia Nigra	brain
26	chr4:87715800-87737400	Weak transcription	Colon Smooth Muscle	Colon
27	chr4:87717200-87737000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr4:87717600-87730800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr4:87717600-87731000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr4:87717800-87732400	Weak transcription	Fetal Thymus	thymus
31	chr4:87718000-87732400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr4:87719200-87738600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr4:87719400-87738000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr4:87720000-87736200	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr4:87720800-87732200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr4:87721800-87733600	Weak transcription	Fetal Stomach	stomach
37	chr4:87722200-87730600	Weak transcription	Esophagus	oesophagus
38	chr4:87722400-87728800	Weak transcription	Brain Hippocampus Middle	brain
39	chr4:87722600-87736400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
40	chr4:87722800-87728800	Weak transcription	Osteobl	bone
41	chr4:87723800-87736200	Strong transcription	HUES64 Cell Line	embryonic stem cell
42	chr4:87723800-87736200	Weak transcription	Fetal Brain Female	brain
43	chr4:87724000-87728800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr4:87724000-87737000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr4:87724600-87737600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr4:87724800-87734400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr4:87724800-87736400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr4:87725000-87730600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr4:87725000-87734000	Strong transcription	NHDF-Ad	bronchial
50	chr4:87725600-87731000	Weak transcription	Brain Cingulate Gyrus	brain

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