Variant report

Variant	rs3817929
Chromosome Location	chr6:142751062-142751063
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs1040525	0.91[CHB][hapmap];0.81[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1040526	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1342060	0.90[CEU][hapmap];0.82[CHB][hapmap];0.88[EUR][1000 genomes]
rs1360194	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1418201	0.90[CEU][hapmap];0.87[CHB][hapmap];0.82[JPT][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs155259	0.89[EUR][1000 genomes]
rs1891308	0.86[CHB][hapmap];0.81[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2039986	0.90[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2039987	0.84[CEU][hapmap];0.82[CHB][hapmap];0.86[EUR][1000 genomes]
rs2050157	0.91[CHB][hapmap];0.81[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2294764	0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2294771	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs262115	0.82[EUR][1000 genomes]
rs262119	0.89[EUR][1000 genomes]
rs262121	0.89[EUR][1000 genomes]
rs262129	0.89[EUR][1000 genomes]
rs263178	0.87[EUR][1000 genomes]
rs263179	0.87[EUR][1000 genomes]
rs263180	0.89[EUR][1000 genomes]
rs263181	0.89[EUR][1000 genomes]
rs263182	0.89[EUR][1000 genomes]
rs263183	0.89[EUR][1000 genomes]
rs263184	0.89[EUR][1000 genomes]
rs263185	0.87[EUR][1000 genomes]
rs263186	0.89[EUR][1000 genomes]
rs263187	0.89[EUR][1000 genomes]
rs263188	0.89[EUR][1000 genomes]
rs263189	0.89[EUR][1000 genomes]
rs3748069	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4896582	0.89[EUR][1000 genomes]
rs611802	0.85[EUR][1000 genomes]
rs6570507	0.95[CHB][hapmap];0.81[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6570508	0.89[EUR][1000 genomes]
rs6570509	0.85[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6570510	0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6909857	0.90[CEU][hapmap];0.90[CHB][hapmap];0.82[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6929442	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6937121	0.90[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7741741	0.82[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7753012	0.90[CEU][hapmap]
rs7754638	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7755109	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7756305	0.90[CEU][hapmap];0.82[CHB][hapmap];0.88[EUR][1000 genomes]
rs7763064	0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7770386	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7774095	0.86[CHB][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7776375	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9373346	0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9389984	0.87[EUR][1000 genomes]
rs9389985	0.83[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9389986	0.81[CEU][hapmap];0.91[CHB][hapmap];0.82[JPT][hapmap];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9389987	0.89[EUR][1000 genomes]
rs9399401	0.90[CEU][hapmap];0.82[CHB][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9403380	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9403381	0.82[CHB][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9403382	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9403383	0.91[CHB][hapmap];0.81[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9403387	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9496346	0.95[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9496369	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9496374	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9496392	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs962554	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs972982	0.90[CEU][hapmap];0.91[CHB][hapmap];0.81[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[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	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

No data

Chromatin state (count:32 , 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	chr6:142748000-142782600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr6:142749000-142758600	Weak transcription	A549	lung
16	chr6:142749200-142754400	Weak transcription	Fetal Lung	lung
17	chr6:142749200-142759600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr6:142749200-142760000	Weak transcription	HSMM	muscle
19	chr6:142749200-142764600	Weak transcription	Primary hematopoietic stem cells	blood
20	chr6:142750000-142752400	Weak transcription	Liver	Liver
21	chr6:142750000-142754800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr6:142750000-142754800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr6:142750000-142754800	Weak transcription	Fetal Intestine Small	intestine
24	chr6:142750000-142755400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr6:142750000-142758600	Weak transcription	HUVEC	blood vessel
26	chr6:142750000-142762200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr6:142750000-142766000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr6:142750200-142751200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr6:142750400-142752200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
30	chr6:142750600-142754200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr6:142751000-142751600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr6:142751000-142754000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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