Variant report

Variant	rs10205556
Chromosome Location	chr2:40645935-40645936
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11901878	1.00[CHB][hapmap];0.94[CHD][hapmap];0.90[ASN][1000 genomes]
rs12052649	0.90[CHB][hapmap];0.88[JPT][hapmap]
rs12052650	0.90[CHB][hapmap]
rs12052800	0.85[CHB][hapmap]
rs12105764	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12988659	0.90[CHB][hapmap];0.83[JPT][hapmap]
rs13017237	0.85[CHB][hapmap]
rs13414307	0.83[CHB][hapmap];0.83[CHD][hapmap];0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs13418726	0.89[CHB][hapmap];0.83[CHD][hapmap]
rs17025965	0.90[CHB][hapmap]
rs2888677	0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2888678	0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs4366950	0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4952621	0.90[CHB][hapmap];0.83[JPT][hapmap]
rs6712702	0.95[CHB][hapmap];0.94[CHD][hapmap];0.89[ASN][1000 genomes]
rs6737011	0.89[CHB][hapmap]
rs7579930	0.89[CHB][hapmap]
rs7598773	0.89[CHB][hapmap];0.83[CHD][hapmap]
rs9789737	0.81[CHB][hapmap]
rs9789739	0.85[CHB][hapmap]

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	nsv529606	chr2:40206280-40896881	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv873911	chr2:40423454-41161464	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	esv2757794	chr2:40547947-40733776	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	esv2759044	chr2:40547947-40733776	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv873916	chr2:40607504-40649084	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv1007027	chr2:40627475-40649916	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10205556	QPCT	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:40623600-40655000	Weak transcription	Primary monocytes fromperipheralblood	blood
2	chr2:40635800-40652600	Weak transcription	Monocytes-CD14+_RO01746	blood
3	chr2:40636200-40646000	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr2:40637200-40646000	Weak transcription	Right Ventricle	heart
5	chr2:40637200-40649000	Weak transcription	Dnd41	blood
6	chr2:40640000-40646600	Weak transcription	Osteobl	bone
7	chr2:40640000-40647600	Weak transcription	NHLF	lung
8	chr2:40641200-40647600	Weak transcription	Fetal Kidney	kidney
9	chr2:40642800-40654600	Weak transcription	HSMM	muscle
10	chr2:40643200-40646000	Weak transcription	Fetal Brain Male	brain
11	chr2:40644200-40656000	Weak transcription	HMEC	breast
12	chr2:40644200-40656400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr2:40644200-40658600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr2:40644800-40646400	Genic enhancers	Fetal Heart	heart
15	chr2:40645000-40649600	Enhancers	Fetal Stomach	stomach
16	chr2:40645400-40646200	Enhancers	Right Atrium	heart
17	chr2:40645400-40646400	Enhancers	Left Ventricle	heart
18	chr2:40645400-40649800	Enhancers	Colon Smooth Muscle	Colon
19	chr2:40645600-40646400	Enhancers	Duodenum Smooth Muscle	Duodenum
20	chr2:40645600-40646400	Enhancers	Placenta Amnion	Placenta Amnion
21	chr2:40645600-40646600	Enhancers	Fetal Lung	lung
22	chr2:40645600-40646800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr2:40645600-40646800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr2:40645600-40646800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr2:40645600-40646800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
26	chr2:40645600-40647000	Enhancers	Brain Anterior Caudate	brain
27	chr2:40645600-40648400	Enhancers	NHDF-Ad	bronchial
28	chr2:40645600-40650000	Enhancers	Rectal Smooth Muscle	rectum
29	chr2:40645800-40646000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
30	chr2:40645800-40646000	Enhancers	Stomach Smooth Muscle	stomach
31	chr2:40645800-40646200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr2:40645800-40646200	Enhancers	Muscle Satellite Cultured Cells	--
33	chr2:40645800-40646200	Enhancers	Small Intestine	intestine
34	chr2:40645800-40646600	Enhancers	Fetal Brain Female	brain

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