Variant report

Variant	rs17763077
Chromosome Location	chr6:71446581-71446582
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11752509	1.00[CEU][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13196394	1.00[CEU][hapmap];0.92[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13197338	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs13198627	0.81[EUR][1000 genomes]
rs13202113	0.99[EUR][1000 genomes]
rs13203355	0.98[EUR][1000 genomes]
rs13212771	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs2474914	0.85[LWK][hapmap];0.82[YRI][hapmap]
rs34336229	0.98[EUR][1000 genomes]
rs34519120	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35293093	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35528153	0.86[ASN][1000 genomes]
rs4706459	0.89[ASN][1000 genomes]
rs4707848	0.86[ASN][1000 genomes]
rs67594983	0.87[ASN][1000 genomes]
rs68097508	0.86[EUR][1000 genomes]
rs9354939	0.85[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.91[ASN][1000 genomes]
rs9354940	0.89[CHB][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.82[YRI][hapmap]
rs9680	0.92[CEU][hapmap];0.93[GIH][hapmap];0.89[TSI][hapmap];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
5	nsv886147	chr6:71273253-71471863	Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17763077	COL19A1	cis	parietal	SCAN
rs17763077	B3GAT2	cis	cerebellum	SCAN

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:71426200-71451000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:71428200-71476400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr6:71435400-71451000	Weak transcription	Fetal Thymus	thymus
4	chr6:71435400-71451000	Weak transcription	Ovary	ovary
5	chr6:71435400-71451200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr6:71435800-71450400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr6:71435800-71477600	Weak transcription	HSMM	muscle
8	chr6:71436000-71449800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr6:71436200-71446600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr6:71436200-71450200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr6:71436200-71451000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr6:71436200-71451400	Weak transcription	Brain Hippocampus Middle	brain
13	chr6:71436200-71452200	Weak transcription	A549	lung
14	chr6:71436200-71453600	Weak transcription	Brain Substantia Nigra	brain
15	chr6:71436200-71470200	Weak transcription	NHDF-Ad	bronchial
16	chr6:71436800-71446800	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr6:71437200-71464800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr6:71437600-71451200	Weak transcription	Esophagus	oesophagus
19	chr6:71438000-71451200	Weak transcription	Brain Angular Gyrus	brain
20	chr6:71438200-71453200	Weak transcription	Brain Anterior Caudate	brain
21	chr6:71438400-71452600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr6:71438400-71468000	Weak transcription	Colon Smooth Muscle	Colon
23	chr6:71438400-71474000	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr6:71439600-71474800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr6:71439800-71457000	Weak transcription	Right Ventricle	heart
26	chr6:71440000-71451000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr6:71440000-71451200	Weak transcription	Gastric	stomach
28	chr6:71440400-71488800	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr6:71440800-71451200	Weak transcription	Fetal Muscle Leg	muscle
30	chr6:71441600-71451000	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr6:71441600-71451200	Weak transcription	Fetal Lung	lung
32	chr6:71441800-71446800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr6:71441800-71453000	Weak transcription	Colonic Mucosa	Colon
34	chr6:71441800-71474200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr6:71442400-71451600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr6:71442400-71453200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr6:71442400-71453600	Weak transcription	Spleen	Spleen
38	chr6:71442600-71453400	Weak transcription	Placenta	Placenta
39	chr6:71442800-71451200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr6:71442800-71458800	Weak transcription	Stomach Smooth Muscle	stomach
41	chr6:71443000-71451000	Weak transcription	Fetal Brain Female	brain
42	chr6:71443200-71488800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr6:71443400-71451200	Weak transcription	Thymus	Thymus
44	chr6:71443400-71466000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr6:71443600-71457000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
46	chr6:71443800-71451000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr6:71443800-71451000	Weak transcription	Brain Germinal Matrix	brain
48	chr6:71444400-71447200	Weak transcription	NH-A	brain
49	chr6:71444400-71449800	Weak transcription	Fetal Intestine Small	intestine
50	chr6:71444400-71450200	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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