Variant report

Variant	rs6570507
Chromosome Location	chr6:142679572-142679573
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 69 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs1040525	0.94[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1040526	0.89[CEU][hapmap];0.95[CHB][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10457739	1.00[YRI][hapmap]
rs11755163	1.00[YRI][hapmap]
rs1342060	0.89[CEU][hapmap];0.86[CHB][hapmap];0.91[GIH][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes]
rs1360194	0.89[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1418201	0.89[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs155259	0.85[EUR][1000 genomes]
rs1891308	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2039986	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2039987	0.87[CEU][hapmap];0.86[CHB][hapmap];0.92[EUR][1000 genomes]
rs2050157	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs225647	1.00[YRI][hapmap]
rs225694	1.00[YRI][hapmap]
rs2294764	0.89[CEU][hapmap];0.90[CHB][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2294771	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs262119	0.85[EUR][1000 genomes]
rs262121	0.85[EUR][1000 genomes]
rs262129	0.85[EUR][1000 genomes]
rs263178	0.83[EUR][1000 genomes]
rs263179	0.83[EUR][1000 genomes]
rs263180	0.85[EUR][1000 genomes]
rs263181	0.85[EUR][1000 genomes]
rs263182	0.85[EUR][1000 genomes]
rs263183	0.85[EUR][1000 genomes]
rs263184	0.85[EUR][1000 genomes]
rs263185	0.82[EUR][1000 genomes]
rs263186	0.85[EUR][1000 genomes]
rs263187	0.85[EUR][1000 genomes]
rs263188	0.85[EUR][1000 genomes]
rs263189	0.85[EUR][1000 genomes]
rs3748069	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3817929	0.95[CHB][hapmap];0.81[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4896582	0.88[CEU][hapmap];0.96[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs611802	0.81[EUR][1000 genomes]
rs6570508	0.91[ASW][hapmap];0.84[GIH][hapmap];1.00[LWK][hapmap];0.97[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs6570509	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6570510	1.00[CEU][hapmap];0.90[CHB][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6909857	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6929442	0.83[CEU][hapmap];0.90[CHB][hapmap];0.80[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6937121	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.98[TSI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7741741	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7753012	0.91[ASW][hapmap];0.82[GIH][hapmap];1.00[LWK][hapmap];0.97[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap]
rs7754638	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7755109	0.84[CEU][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];0.89[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7756305	0.89[CEU][hapmap];0.86[CHB][hapmap];0.91[GIH][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes]
rs7763064	0.90[EUR][1000 genomes]
rs7770386	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7774095	0.94[CEU][hapmap];0.90[CHB][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7776375	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9373346	1.00[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9389984	0.91[EUR][1000 genomes]
rs9389985	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9389986	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9389987	0.94[EUR][1000 genomes]
rs9399401	0.89[CEU][hapmap];0.86[CHB][hapmap];0.92[EUR][1000 genomes]
rs9403380	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9403381	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[GIH][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes]
rs9403382	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9403383	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9403387	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9496346	0.84[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9496369	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9496374	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9496392	0.90[EUR][1000 genomes]
rs962554	0.84[CEU][hapmap];0.95[CHB][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs972982	0.89[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[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

Variant related diseases (count:4)

Disease	PMID	Source
Height	25429064	GWAS catalog
Height	20397748	GWAS catalog
Height	19343178	GWAS catalog
Scoliosis	23666238	GWAS catalog

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:142665600-142680200	Weak transcription	HUVEC	blood vessel
2	chr6:142672600-142680800	Weak transcription	Fetal Brain Male	brain
3	chr6:142674800-142680400	Enhancers	Fetal Lung	lung
4	chr6:142676400-142681000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr6:142676800-142688600	Weak transcription	Fetal Heart	heart
6	chr6:142677000-142682000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr6:142677000-142682000	Weak transcription	Placenta	Placenta
8	chr6:142677400-142679800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr6:142677600-142681400	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr6:142677600-142682200	Enhancers	A549	lung
11	chr6:142677800-142679600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr6:142677800-142680200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr6:142677800-142680200	Weak transcription	Fetal Intestine Small	intestine
14	chr6:142677800-142681000	Enhancers	Primary hematopoietic stem cells	blood
15	chr6:142677800-142682400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr6:142677800-142682400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr6:142678000-142679600	Weak transcription	Fetal Thymus	thymus
18	chr6:142678000-142679600	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr6:142678000-142680400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr6:142678000-142680400	Weak transcription	Thymus	Thymus
21	chr6:142678000-142682400	Weak transcription	HMEC	breast
22	chr6:142678800-142680000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr6:142679000-142679600	Enhancers	Fetal Kidney	kidney
24	chr6:142679000-142679600	Genic enhancers	HepG2	liver
25	chr6:142679000-142679600	Genic enhancers	NHLF	lung
26	chr6:142679000-142682200	Weak transcription	Fetal Intestine Large	intestine
27	chr6:142679200-142679600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr6:142679200-142679600	Enhancers	HSMM	muscle
29	chr6:142679200-142679800	Enhancers	Cortex derived primary cultured neurospheres	brain
30	chr6:142679200-142680200	Weak transcription	NHEK	skin
31	chr6:142679200-142681000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr6:142679200-142681200	Enhancers	Primary T cells from cord blood	blood
33	chr6:142679400-142680800	Enhancers	Liver	Liver
34	chr6:142679400-142681200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr6:142679400-142684800	Weak transcription	Fetal Brain Female	brain
36	chr6:142679400-142688200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr6:142679400-142693200	Weak transcription	Hela-S3	cervix

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