Variant report

Variant	rs12774901
Chromosome Location	chr10:96329550-96329551
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1042192	0.97[CHD][hapmap];0.88[GIH][hapmap]
rs1042194	0.81[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap]
rs1048196	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10509676	0.82[CHB][hapmap];0.86[YRI][hapmap]
rs1065027	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11594492	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11595478	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs12570771	0.81[AFR][1000 genomes]
rs12571306	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12571659	0.87[EUR][1000 genomes]
rs12768009	0.85[GIH][hapmap];0.86[YRI][hapmap]
rs12769392	0.80[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs12770064	1.00[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.87[EUR][1000 genomes]
rs12773342	0.82[CHB][hapmap];0.86[YRI][hapmap]
rs12774450	0.85[AFR][1000 genomes]
rs12783717	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12784245	0.82[AFR][1000 genomes]
rs1326832	0.82[CHB][hapmap]
rs1926711	0.85[GIH][hapmap]
rs1926712	0.82[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap]
rs2025445	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2031322	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs2151953	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.80[EUR][1000 genomes]
rs2281890	0.82[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap]
rs2281891	0.86[ASW][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];0.93[LWK][hapmap];0.96[MKK][hapmap];0.86[YRI][hapmap]
rs2296680	0.82[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap]
rs2860838	0.82[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap]
rs34151925	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35134124	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35602247	0.83[EUR][1000 genomes]
rs35805353	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4986894	0.82[CHB][hapmap];0.94[CHD][hapmap];0.88[GIH][hapmap];0.93[LWK][hapmap];0.96[MKK][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes]
rs7082105	0.84[EUR][1000 genomes]
rs7085890	0.82[CHB][hapmap]
rs7089349	0.84[AFR][1000 genomes]
rs7100783	0.82[CHB][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes]
rs717238	0.82[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap]
rs7900135	0.82[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap]
rs932809	0.82[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv497859	chr10:96058024-97027747	Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	esv1819509	chr10:96064300-96361776	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1053747	chr10:96211618-96366396	Strong transcription ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12774901	CYP2C19	cis	Esophagus Mucosa	GTEx
rs12774901	GOLGA7B	cis	parietal	SCAN
rs12774901	HELLS	cis	cerebellum	SCAN
rs12774901	ZFYVE27	cis	parietal	SCAN

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:96306400-96330600	Weak transcription	Placenta	Placenta
2	chr10:96306400-96357200	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr10:96306400-96365600	Weak transcription	Esophagus	oesophagus
4	chr10:96306400-96370400	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr10:96306400-96370600	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr10:96306400-96371000	Weak transcription	Ovary	ovary
7	chr10:96306600-96349800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr10:96306600-96353800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr10:96306600-96379200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr10:96306800-96330400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr10:96306800-96348000	Weak transcription	Primary monocytes fromperipheralblood	blood
12	chr10:96306800-96348200	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr10:96306800-96348400	Weak transcription	Primary B cells from cord blood	blood
14	chr10:96306800-96349800	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr10:96306800-96357200	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr10:96306800-96373000	Weak transcription	Primary T cells from cord blood	blood
17	chr10:96307000-96358200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr10:96307000-96375000	Weak transcription	Osteobl	bone
19	chr10:96307200-96371200	Weak transcription	Fetal Brain Male	brain
20	chr10:96307600-96356000	Weak transcription	NHDF-Ad	bronchial
21	chr10:96307600-96373200	Weak transcription	Brain Germinal Matrix	brain
22	chr10:96307800-96348200	Weak transcription	NHEK	skin
23	chr10:96307800-96373000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr10:96308000-96373200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr10:96309400-96340800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr10:96309400-96354000	Weak transcription	K562	blood
27	chr10:96309600-96372800	Strong transcription	HUES6 Cell Line	embryonic stem cell
28	chr10:96309600-96377000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr10:96310200-96339800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
30	chr10:96310400-96339800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr10:96312200-96334400	Strong transcription	A549	lung
32	chr10:96312200-96354000	Weak transcription	Gastric	stomach
33	chr10:96312800-96372200	Strong transcription	Dnd41	blood
34	chr10:96314000-96330800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr10:96314200-96339800	Strong transcription	Fetal Thymus	thymus
36	chr10:96314200-96373400	Strong transcription	HUES64 Cell Line	embryonic stem cell
37	chr10:96315000-96369200	Weak transcription	Fetal Kidney	kidney
38	chr10:96315200-96332200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
39	chr10:96315600-96343800	Strong transcription	H1 Cell Line	embryonic stem cell
40	chr10:96315600-96345200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr10:96316000-96330200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr10:96316000-96338200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr10:96316000-96371400	Weak transcription	Fetal Brain Female	brain
44	chr10:96316000-96374000	Strong transcription	HUES48 Cell Line	embryonic stem cell
45	chr10:96316200-96357600	Weak transcription	Duodenum Mucosa	Duodenum
46	chr10:96316200-96373000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
47	chr10:96317000-96332600	Strong transcription	ES-I3 Cell Line	embryonic stem cell
48	chr10:96317000-96372600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
49	chr10:96317400-96348000	Weak transcription	NH-A	brain
50	chr10:96318400-96330000	Strong transcription	Fetal Stomach	stomach

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