Variant report

Variant	rs195092
Chromosome Location	chr6:119628029-119628030
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:119617703..119620328-chr6:119627300..119629945,2	K562	blood:
2	chr6:119609733..119612979-chr6:119627928..119630973,3	K562	blood:
3	chr6:119590465..119593242-chr6:119626545..119629330,2	K562	blood:

Variant related genes	Relation type
ENSG00000216316	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11962211	0.80[MEX][hapmap];0.84[MKK][hapmap]
rs12209570	0.91[CHB][hapmap];0.91[CHD][hapmap];0.81[GIH][hapmap];0.87[JPT][hapmap]
rs12215906	0.87[ASN][1000 genomes]
rs1295391	0.89[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap]
rs1295392	0.86[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs1324554	0.84[EUR][1000 genomes]
rs195048	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs195056	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs195058	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs195090	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2057554	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2267673	0.82[EUR][1000 genomes]
rs2267674	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2267675	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2267676	0.81[ASN][1000 genomes]
rs2299878	0.96[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2299886	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2357164	0.96[CEU][hapmap];0.81[JPT][hapmap];0.95[YRI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3778111	0.81[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.86[YRI][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3819731	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4946406	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6569074	0.86[YRI][hapmap]
rs6937640	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7755155	0.92[CEU][hapmap];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7755572	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9374788	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9489630	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9489638	0.96[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs975578	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025995	chr6:119407742-119709548	Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv1017507	chr6:119465981-119664949	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	esv3447598	chr6:119558591-120119384	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	esv3389526	chr6:119558598-120190087	ZNF genes & repeats Enhancers Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	esv1803720	chr6:119609322-119628198	Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	esv1794477	chr6:119609322-119633534	Strong transcription Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs195092	GPRC6A	cis	cerebellum	SCAN
rs195092	ASF1A	cis	cerebellum	SCAN

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:119592400-119633600	Weak transcription	Primary T cells from cord blood	blood
2	chr6:119599800-119632600	Weak transcription	Spleen	Spleen
3	chr6:119600000-119629000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr6:119602400-119629200	Weak transcription	NH-A	brain
5	chr6:119602600-119629000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr6:119602600-119635600	Weak transcription	Esophagus	oesophagus
7	chr6:119607600-119628600	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr6:119614200-119629000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr6:119615400-119632600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr6:119616400-119630200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr6:119617200-119637400	Weak transcription	Aorta	Aorta
12	chr6:119617400-119628200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr6:119617600-119629000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr6:119617600-119632200	Weak transcription	Right Ventricle	heart
15	chr6:119618000-119629000	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr6:119618000-119629200	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr6:119618000-119630200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr6:119618200-119633800	Weak transcription	Colonic Mucosa	Colon
19	chr6:119618600-119629200	Weak transcription	Primary neutrophils fromperipheralblood	blood
20	chr6:119618600-119630200	Weak transcription	Small Intestine	intestine
21	chr6:119619400-119632800	Weak transcription	Ovary	ovary
22	chr6:119621000-119628200	Strong transcription	Liver	Liver
23	chr6:119621600-119633600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr6:119621600-119634000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr6:119621800-119629600	Weak transcription	Fetal Intestine Small	intestine
26	chr6:119623000-119630200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr6:119623000-119632000	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr6:119623400-119633600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr6:119624000-119628200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
30	chr6:119624400-119629000	Weak transcription	HUVEC	blood vessel
31	chr6:119625200-119629000	Weak transcription	NHEK	skin
32	chr6:119625200-119629200	Weak transcription	NHLF	lung
33	chr6:119625200-119631600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr6:119625200-119631600	Genic enhancers	K562	blood
35	chr6:119625200-119632800	Weak transcription	Right Atrium	heart
36	chr6:119625200-119634200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr6:119625200-119634200	Weak transcription	Brain Angular Gyrus	brain
38	chr6:119625200-119634400	Weak transcription	Fetal Stomach	stomach
39	chr6:119625200-119634400	Weak transcription	Thymus	Thymus
40	chr6:119625200-119635600	Weak transcription	Psoas Muscle	Psoas
41	chr6:119625200-119668600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr6:119625800-119628600	Strong transcription	Primary hematopoietic stem cells	blood
43	chr6:119626400-119628200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr6:119626400-119628200	Strong transcription	Fetal Thymus	thymus
45	chr6:119626400-119629400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr6:119626600-119628200	Strong transcription	Primary B cells from cord blood	blood
47	chr6:119626600-119628200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr6:119626600-119628200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr6:119626600-119628200	Strong transcription	Adipose Nuclei	Adipose
50	chr6:119626600-119628200	Strong transcription	Duodenum Mucosa	Duodenum

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