Variant report

Variant	rs10231916
Chromosome Location	chr7:96763456-96763457
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1014341	0.84[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.85[ASN][1000 genomes]
rs10229181	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.97[TSI][hapmap];0.83[ASN][1000 genomes]
rs10235199	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap];0.97[TSI][hapmap];0.83[ASN][1000 genomes]
rs10246622	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10252102	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10260298	0.89[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.85[ASN][1000 genomes]
rs10274547	0.80[ASN][1000 genomes]
rs10275135	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10279603	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11972232	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11980904	0.82[ASN][1000 genomes]
rs1199289	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs1199290	0.85[ASN][1000 genomes]
rs1199291	0.85[ASN][1000 genomes]
rs1199292	0.84[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.97[TSI][hapmap];0.85[ASN][1000 genomes]
rs12056091	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12669915	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12670377	0.82[CHD][hapmap]
rs12671362	0.84[ASN][1000 genomes]
rs13475	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.83[ASN][1000 genomes]
rs1534370	0.84[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.95[TSI][hapmap];0.84[ASN][1000 genomes]
rs1880732	0.81[AFR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1917941	0.83[ASN][1000 genomes]
rs2140954	0.86[CHB][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2693313	0.96[CEU][hapmap]
rs28646010	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28825121	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4729330	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6465571	0.84[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.95[TSI][hapmap];0.84[ASN][1000 genomes]
rs6943457	0.83[ASN][1000 genomes]
rs6958059	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6961807	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6963921	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6973369	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.84[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73233819	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7787376	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7794886	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7803945	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7810432	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7811797	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9656043	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1019725	chr7:96749866-96850819	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv539029	chr7:96749866-96850819	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10231916	ACN9	cis	parietal	SCAN
rs10231916	AP4M1	cis	cerebellum	SCAN
rs10231916	AZGP1	cis	cerebellum	SCAN
rs10231916	ZNF655	cis	parietal	SCAN

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:96747600-96768200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr7:96747800-96768200	Weak transcription	Aorta	Aorta
3	chr7:96748400-96767200	Weak transcription	Fetal Stomach	stomach
4	chr7:96748400-96768200	Weak transcription	Right Ventricle	heart
5	chr7:96748400-96768400	Weak transcription	Psoas Muscle	Psoas
6	chr7:96749000-96768200	Weak transcription	Right Atrium	heart
7	chr7:96749200-96768000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr7:96749400-96768000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr7:96749400-96768200	Weak transcription	Primary T cells from cord blood	blood
10	chr7:96752400-96766000	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr7:96755000-96766800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr7:96755000-96768000	Weak transcription	Adipose Nuclei	Adipose
13	chr7:96756200-96767800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr7:96756400-96765600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr7:96756600-96766400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr7:96756600-96768000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr7:96756600-96768000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr7:96759200-96768400	Weak transcription	Brain Hippocampus Middle	brain
19	chr7:96760000-96767200	Weak transcription	Fetal Intestine Small	intestine
20	chr7:96760000-96768000	Weak transcription	Duodenum Mucosa	Duodenum
21	chr7:96760000-96768000	Weak transcription	Spleen	Spleen
22	chr7:96760000-96768200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr7:96760000-96768200	Weak transcription	Esophagus	oesophagus
24	chr7:96760200-96767800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr7:96760200-96768000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr7:96760200-96768200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr7:96760400-96766400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr7:96760400-96766600	Weak transcription	K562	blood
29	chr7:96760400-96767400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr7:96760400-96768000	Weak transcription	Liver	Liver
31	chr7:96760400-96768000	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr7:96760400-96768200	Weak transcription	Gastric	stomach
33	chr7:96760400-96768200	Weak transcription	Left Ventricle	heart
34	chr7:96760400-96796800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr7:96762200-96763600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr7:96762200-96763600	Enhancers	Brain Germinal Matrix	brain
37	chr7:96762200-96764800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr7:96762400-96763600	Enhancers	HepG2	liver
39	chr7:96762400-96764400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr7:96762400-96764600	Enhancers	Cortex derived primary cultured neurospheres	brain
41	chr7:96762400-96766400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr7:96762600-96763600	Enhancers	Breast Myoepithelial Primary Cells	Breast
43	chr7:96762800-96763600	Enhancers	Brain Anterior Caudate	brain
44	chr7:96762800-96766600	Weak transcription	Primary B cells from cord blood	blood
45	chr7:96762800-96768200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr7:96762800-96768600	Weak transcription	Fetal Lung	lung
47	chr7:96763000-96764200	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr7:96763000-96766400	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr7:96763200-96764400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr7:96763200-96766800	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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