Variant report

Variant	rs6569716
Chromosome Location	chr6:131312729-131312730
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:131308949..131310454-chr6:131311371..131314255,2	K562	blood:
2	chr6:131304583..131308500-chr6:131310186..131313138,4	K562	blood:
3	chr6:131301483..131303877-chr6:131310985..131313836,2	MCF-7	breast:
4	chr6:131308949..131310665-chr6:131311371..131314257,2	K562	blood:

Extended variants
information (count: 60 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs1043598	0.93[CHD][hapmap];0.92[JPT][hapmap]
rs10499174	0.92[JPT][hapmap]
rs12661081	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12664355	0.93[CHD][hapmap];0.92[JPT][hapmap]
rs12965	0.93[CHD][hapmap];0.92[JPT][hapmap]
rs13193246	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1332490	0.84[CEU][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes]
rs1332491	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1338905	0.87[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];0.94[MKK][hapmap];0.86[TSI][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17059681	0.93[CHD][hapmap];0.92[JPT][hapmap]
rs17059683	0.92[JPT][hapmap]
rs17059698	0.92[JPT][hapmap]
rs17059702	0.92[JPT][hapmap]
rs17059896	0.92[JPT][hapmap];0.99[ASN][1000 genomes]
rs17059925	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs17831009	0.92[JPT][hapmap]
rs1855077	0.86[AFR][1000 genomes]
rs1888959	0.84[CEU][hapmap];0.81[GIH][hapmap];0.84[TSI][hapmap];0.80[EUR][1000 genomes]
rs1976982	0.84[ASN][1000 genomes]
rs1977578	0.81[EUR][1000 genomes]
rs2007339	0.87[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2151069	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2225557	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2275063	0.92[JPT][hapmap]
rs2275065	0.81[ASN][1000 genomes]
rs2327005	0.81[EUR][1000 genomes]
rs3777450	0.92[JPT][hapmap];0.81[ASN][1000 genomes]
rs3777453	0.86[CHB][hapmap];0.92[JPT][hapmap];0.81[ASN][1000 genomes]
rs3777463	0.88[CHB][hapmap];0.93[CHD][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs3822864	0.92[JPT][hapmap];0.81[ASN][1000 genomes]
rs4895902	0.84[CEU][hapmap];0.89[CHB][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4897480	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4897481	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4897482	0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4897490	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56027377	0.81[ASN][1000 genomes]
rs6569718	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6569720	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6569722	0.91[ASN][1000 genomes]
rs6569725	0.91[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs6900810	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6908917	0.84[CEU][hapmap];0.81[GIH][hapmap];0.84[TSI][hapmap]
rs6928986	0.89[ASW][hapmap];0.84[CEU][hapmap];0.81[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs6932317	0.81[EUR][1000 genomes]
rs6942081	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73623428	0.99[ASN][1000 genomes]
rs73774307	0.81[ASN][1000 genomes]
rs73774328	0.91[ASN][1000 genomes]
rs7742376	0.84[CEU][hapmap];0.81[GIH][hapmap];0.84[TSI][hapmap]
rs7747881	0.88[CHB][hapmap];0.92[JPT][hapmap];0.86[ASN][1000 genomes]
rs7765007	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7765757	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7769153	0.88[CHB][hapmap];0.93[CHD][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs9321268	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9372988	0.87[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9402307	0.81[EUR][1000 genomes]
rs9483203	0.81[EUR][1000 genomes]
rs9689026	0.80[EUR][1000 genomes];0.91[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	nsv1032955	chr6:131298803-131818502	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv538443	chr6:131298803-131818502	Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6569716	AKAP7	cis	multi-tissue	Pritchard
rs6569716	THEMIS	cis	cerebellum	SCAN
rs6569716	TAAR1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:131298800-131314800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr6:131300400-131314600	Weak transcription	Small Intestine	intestine
3	chr6:131303800-131315400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr6:131304200-131313400	Weak transcription	K562	blood
5	chr6:131306800-131313800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr6:131306800-131313800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr6:131306800-131315200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr6:131306800-131317000	Weak transcription	Fetal Intestine Small	intestine
9	chr6:131306800-131317200	Weak transcription	NHLF	lung
10	chr6:131306800-131317400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr6:131306800-131320000	Weak transcription	Left Ventricle	heart
12	chr6:131308000-131315400	Weak transcription	Lung	lung
13	chr6:131308600-131314400	Weak transcription	Dnd41	blood
14	chr6:131309200-131317200	Weak transcription	Adipose Nuclei	Adipose
15	chr6:131310400-131316800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr6:131311200-131313400	Weak transcription	HepG2	liver
17	chr6:131311400-131318400	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr6:131312200-131313000	Enhancers	Fetal Kidney	kidney
19	chr6:131312200-131313600	Enhancers	Fetal Lung	lung
20	chr6:131312200-131314000	Enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr6:131312400-131313400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr6:131312400-131313800	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr6:131312400-131314000	Weak transcription	Pancreas	Pancrea
24	chr6:131312400-131314600	Weak transcription	Right Atrium	heart
25	chr6:131312400-131317000	Weak transcription	Rectal Smooth Muscle	rectum
26	chr6:131312400-131318400	Weak transcription	Fetal Muscle Leg	muscle
27	chr6:131312600-131313600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr6:131312600-131313600	Enhancers	Osteobl	bone
29	chr6:131312600-131314000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr6:131312600-131314800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr6:131312600-131314800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr6:131312600-131317400	Weak transcription	Fetal Stomach	stomach
33	chr6:131312600-131321800	Weak transcription	Skeletal Muscle Male	skeletal muscle

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