Variant report

Variant	rs13212771
Chromosome Location	chr6:71530701-71530702
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:71300001..71302323-chr6:71529917..71532229,2	K562	blood:

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11752509	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs13196394	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs13197338	1.00[CEU][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13198627	0.90[ASN][1000 genomes]
rs13202113	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13203355	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17763077	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs2038477	0.88[JPT][hapmap]
rs2474915	0.83[JPT][hapmap]
rs2474921	0.88[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2504748	0.83[JPT][hapmap]
rs2504750	0.83[JPT][hapmap]
rs2504751	0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs2504752	0.83[JPT][hapmap]
rs34336229	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34519120	0.96[EUR][1000 genomes]
rs35293093	0.96[EUR][1000 genomes]
rs483894	0.83[JPT][hapmap]
rs68097508	0.82[EUR][1000 genomes]
rs9680	0.92[CEU][hapmap];0.83[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932111	chr6:70736835-71633094	Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv1027049	chr6:70961610-71561488	Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv524328	chr6:70961833-71558805	Flanking Bivalent TSS/Enh Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv917312	chr6:70961903-71601688	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13212771	COL19A1	cis	parietal	SCAN
rs13212771	B3GAT2	cis	cerebellum	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:71468800-71532200	Weak transcription	Primary T cells fromperipheralblood	blood
2	chr6:71474600-71568800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr6:71492400-71563600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr6:71505600-71534400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr6:71506800-71570600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr6:71508200-71531400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr6:71508400-71543800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr6:71511600-71554600	Weak transcription	Dnd41	blood
9	chr6:71514800-71535200	Weak transcription	Stomach Smooth Muscle	stomach
10	chr6:71514800-71548400	Weak transcription	Ovary	ovary
11	chr6:71516200-71534600	Weak transcription	Aorta	Aorta
12	chr6:71516200-71534600	Weak transcription	Left Ventricle	heart
13	chr6:71516200-71535000	Weak transcription	Fetal Muscle Trunk	muscle
14	chr6:71516200-71538400	Weak transcription	Esophagus	oesophagus
15	chr6:71516200-71538600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr6:71516200-71546200	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr6:71516400-71532200	Weak transcription	Primary T cells from cord blood	blood
18	chr6:71516400-71535600	Weak transcription	Primary monocytes fromperipheralblood	blood
19	chr6:71516400-71562200	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr6:71516400-71567600	Weak transcription	Pancreas	Pancrea
21	chr6:71516600-71543400	Weak transcription	Adipose Nuclei	Adipose
22	chr6:71516600-71567600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr6:71517000-71531200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr6:71518400-71552400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr6:71520600-71538400	Weak transcription	Fetal Intestine Small	intestine
26	chr6:71521800-71532000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr6:71521800-71532400	Weak transcription	Monocytes-CD14+_RO01746	blood
28	chr6:71522000-71558200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr6:71522200-71532000	Weak transcription	Primary B cells from cord blood	blood
30	chr6:71524600-71548200	Weak transcription	Psoas Muscle	Psoas
31	chr6:71529800-71531200	Enhancers	Liver	Liver
32	chr6:71530600-71531200	Strong transcription	Primary T helper cells fromperipheralblood	blood
33	chr6:71530600-71531200	Enhancers	Stomach Mucosa	stomach
34	chr6:71530600-71532000	Weak transcription	Cortex derived primary cultured neurospheres	brain

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