Variant report

Variant	rs2031322
Chromosome Location	chr10:96289756-96289757
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:96281903..96284503-chr10:96287448..96290180,2	K562	blood:

Extended variants
information (count: 44 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1048196	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs1065027	0.83[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs11187949	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11187998	0.83[LWK][hapmap]
rs11591693	0.84[EUR][1000 genomes]
rs11594492	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs11595478	0.93[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11598738	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12219906	0.81[LWK][hapmap]
rs12569637	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12571306	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12571659	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12766721	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12769392	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12770064	0.94[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12774901	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]
rs12777300	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12783717	0.83[EUR][1000 genomes]
rs12785198	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1326832	0.82[CHB][hapmap]
rs1926711	0.84[CHD][hapmap]
rs1926712	0.82[CHB][hapmap];0.91[CHD][hapmap];0.82[GIH][hapmap]
rs2025445	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs2151952	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2151953	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2296680	0.82[CHB][hapmap];0.92[CHD][hapmap];0.82[GIH][hapmap];0.82[LWK][hapmap]
rs2860838	0.82[CHB][hapmap];0.92[CHD][hapmap];0.82[GIH][hapmap]
rs34151925	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs34320768	0.88[EUR][1000 genomes]
rs34402112	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34560326	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35134124	0.84[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs35602247	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35805353	0.84[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs7082105	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7085890	0.82[CHB][hapmap]
rs7100783	0.82[CHB][hapmap];0.85[YRI][hapmap]
rs717238	0.82[CHB][hapmap];0.92[CHD][hapmap];0.82[GIH][hapmap]
rs7900135	0.82[CHB][hapmap];0.92[CHD][hapmap];0.82[GIH][hapmap]
rs932809	0.82[CHB][hapmap];0.92[CHD][hapmap];0.82[GIH][hapmap]

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	esv2761616	chr10:95966768-96303701	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2031322	HELLS	cis	cerebellum	SCAN
rs2031322	GOLGA7B	cis	parietal	SCAN
rs2031322	CYP2C19	cis	Esophagus Mucosa	GTEx

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:96211600-96292200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr10:96223200-96293600	Weak transcription	NHDF-Ad	bronchial
3	chr10:96244400-96304600	Weak transcription	Aorta	Aorta
4	chr10:96250800-96294000	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr10:96250800-96297400	Weak transcription	Small Intestine	intestine
6	chr10:96257000-96293400	Weak transcription	HepG2	liver
7	chr10:96261000-96304400	Weak transcription	NH-A	brain
8	chr10:96264200-96296800	Weak transcription	Brain Germinal Matrix	brain
9	chr10:96266000-96304600	Weak transcription	Fetal Kidney	kidney
10	chr10:96267400-96303800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr10:96268400-96304400	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr10:96268800-96297200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr10:96268800-96304400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr10:96269600-96292000	Weak transcription	Brain Hippocampus Middle	brain
15	chr10:96270200-96304200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr10:96271800-96294000	Weak transcription	Psoas Muscle	Psoas
17	chr10:96271800-96304000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr10:96272000-96294000	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr10:96272000-96304600	Weak transcription	HSMMtube	muscle
20	chr10:96272200-96295800	Weak transcription	Primary hematopoietic stem cells	blood
21	chr10:96272400-96293000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr10:96272600-96293400	Weak transcription	Primary monocytes fromperipheralblood	blood
23	chr10:96273600-96294000	Weak transcription	Fetal Muscle Trunk	muscle
24	chr10:96274400-96304000	Weak transcription	Stomach Mucosa	stomach
25	chr10:96274400-96304400	Weak transcription	Rectal Smooth Muscle	rectum
26	chr10:96274600-96290800	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr10:96274600-96292400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr10:96274600-96304000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr10:96277000-96292400	Weak transcription	Primary B cells from peripheral blood	blood
30	chr10:96277200-96294000	Weak transcription	Left Ventricle	heart
31	chr10:96278400-96290800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr10:96279600-96297200	Weak transcription	Spleen	Spleen
33	chr10:96280400-96304800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr10:96281400-96294000	Weak transcription	Brain Angular Gyrus	brain
35	chr10:96281400-96294600	Weak transcription	Brain Cingulate Gyrus	brain
36	chr10:96281600-96293600	Weak transcription	Brain Anterior Caudate	brain
37	chr10:96281800-96296800	Weak transcription	Fetal Brain Female	brain
38	chr10:96282000-96293800	Weak transcription	Stomach Smooth Muscle	stomach
39	chr10:96282200-96304200	Weak transcription	Colonic Mucosa	Colon
40	chr10:96282400-96290600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr10:96284000-96293600	Weak transcription	Brain Substantia Nigra	brain
42	chr10:96284000-96304200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr10:96284000-96304400	Weak transcription	Osteobl	bone
44	chr10:96284200-96290400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr10:96284200-96290800	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr10:96284200-96292800	Weak transcription	Duodenum Mucosa	Duodenum
47	chr10:96284200-96294000	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr10:96284200-96297200	Weak transcription	Pancreas	Pancrea
49	chr10:96284200-96299200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr10:96284200-96304400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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