Variant report

Variant	rs3817928
Chromosome Location	chr6:142750516-142750517
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10484733	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11155241	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11155242	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.85[YRI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11759653	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12189838	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12190271	0.81[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.85[YRI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12197866	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12213892	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13198644	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1329705	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1329707	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17071756	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs171891	0.82[EUR][1000 genomes]
rs1928528	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2294775	0.81[ASW][hapmap];0.93[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs262117	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs262118	0.82[EUR][1000 genomes]
rs4304190	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6570511	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6900087	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6900233	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6901807	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6903424	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6906468	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6912639	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6922607	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6925979	0.85[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73780219	1.00[ASN][1000 genomes]
rs73780221	1.00[ASN][1000 genomes]
rs7756434	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7757571	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7765770	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7776356	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9321870	0.84[EUR][1000 genomes]
rs9373347	0.94[EUR][1000 genomes]
rs9403386	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs984932	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	nsv949088	chr6:142561402-143128849	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv830825	chr6:142585242-142752575	Enhancers Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

Variant related diseases (count:2)

Disease	PMID	Source
Pulmonary function (interaction)	23284291	GWAS catalog
Pulmonary function	20010835	GWAS catalog

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:142718000-142763200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr6:142733800-142758000	Weak transcription	Stomach Smooth Muscle	stomach
3	chr6:142735200-142760200	Weak transcription	Esophagus	oesophagus
4	chr6:142735200-142765400	Weak transcription	Hela-S3	cervix
5	chr6:142735800-142765400	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr6:142737600-142765600	Weak transcription	Duodenum Mucosa	Duodenum
7	chr6:142737800-142765800	Weak transcription	Fetal Brain Male	brain
8	chr6:142738000-142774200	Weak transcription	NHEK	skin
9	chr6:142739000-142764800	Weak transcription	NHLF	lung
10	chr6:142743200-142755800	Weak transcription	Placenta	Placenta
11	chr6:142743200-142769200	Weak transcription	HMEC	breast
12	chr6:142743400-142761600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr6:142746000-142751600	Strong transcription	HepG2	liver
14	chr6:142746200-142750600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr6:142748000-142782600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr6:142749000-142758600	Weak transcription	A549	lung
17	chr6:142749200-142751000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr6:142749200-142754400	Weak transcription	Fetal Lung	lung
19	chr6:142749200-142759600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr6:142749200-142760000	Weak transcription	HSMM	muscle
21	chr6:142749200-142764600	Weak transcription	Primary hematopoietic stem cells	blood
22	chr6:142750000-142752400	Weak transcription	Liver	Liver
23	chr6:142750000-142754800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr6:142750000-142754800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr6:142750000-142754800	Weak transcription	Fetal Intestine Small	intestine
26	chr6:142750000-142755400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr6:142750000-142758600	Weak transcription	HUVEC	blood vessel
28	chr6:142750000-142762200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr6:142750000-142766000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr6:142750200-142751000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr6:142750200-142751200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr6:142750400-142751000	Enhancers	Muscle Satellite Cultured Cells	--
33	chr6:142750400-142752200	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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