Variant report

Variant	rs10229181
Chromosome Location	chr7:96795041-96795042
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:96794189..96796264-chr7:96799436..96802402,4	K562	blood:

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

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

rs_ID	r²[population]
rs1014341	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.97[TSI][hapmap];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10231916	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]
rs10233801	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10235199	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10252102	0.85[ASN][1000 genomes]
rs10260298	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10274547	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10275135	0.81[ASN][1000 genomes]
rs10279603	0.83[ASN][1000 genomes]
rs10281783	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11972232	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1199289	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1199290	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1199291	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1199292	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12056091	0.87[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.80[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.85[ASN][1000 genomes]
rs12669915	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12670377	0.82[JPT][hapmap]
rs12671362	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12671685	0.87[YRI][hapmap]
rs13475	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1534370	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1880732	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1917941	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2140954	0.86[CHB][hapmap]
rs2693313	1.00[CEU][hapmap]
rs28646010	0.85[ASN][1000 genomes]
rs28825121	0.81[ASN][1000 genomes]
rs34159711	0.88[AFR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62499473	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6465571	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6943457	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6961807	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6963921	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6973369	0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.90[TSI][hapmap];0.81[ASN][1000 genomes]
rs7787376	0.87[ASW][hapmap];0.88[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.89[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.83[ASN][1000 genomes]
rs7794886	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.97[TSI][hapmap];0.81[ASN][1000 genomes]
rs7803945	0.96[CEU][hapmap];0.85[ASN][1000 genomes]
rs7810432	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.95[TSI][hapmap];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7811797	0.81[ASN][1000 genomes]
rs9656043	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[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
rs10229181	AP4M1	cis	cerebellum	SCAN
rs10229181	AZGP1	cis	cerebellum	SCAN
rs10229181	ZNF655	cis	parietal	SCAN
rs10229181	ACN9	cis	parietal	SCAN

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:96760400-96796800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr7:96768800-96797800	Weak transcription	Left Ventricle	heart
3	chr7:96769000-96799600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr7:96769000-96811600	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr7:96771400-96818200	Weak transcription	A549	lung
6	chr7:96783600-96797000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr7:96785600-96796800	Weak transcription	HepG2	liver
8	chr7:96787000-96795600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr7:96787400-96797600	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr7:96787600-96796200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr7:96787600-96796600	Weak transcription	Esophagus	oesophagus
12	chr7:96789400-96812400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr7:96789400-96815400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr7:96789400-96818000	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr7:96789600-96797000	Weak transcription	Aorta	Aorta
16	chr7:96789600-96797200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr7:96789600-96797200	Weak transcription	Lung	lung
18	chr7:96789600-96805200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr7:96789600-96818400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr7:96790400-96795200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr7:96790400-96814600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr7:96790600-96795200	Weak transcription	K562	blood
23	chr7:96790600-96796400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr7:96790600-96796400	Weak transcription	Dnd41	blood
25	chr7:96790600-96797000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr7:96790600-96811200	Weak transcription	Primary T helper cells fromperipheralblood	blood
27	chr7:96790600-96811600	Weak transcription	Primary T cells fromperipheralblood	blood
28	chr7:96790600-96813600	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr7:96790600-96813600	Weak transcription	Duodenum Mucosa	Duodenum
30	chr7:96790800-96796200	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr7:96790800-96797200	Weak transcription	Primary B cells from cord blood	blood
32	chr7:96790800-96797200	Weak transcription	Primary hematopoietic stem cells	blood
33	chr7:96791000-96796800	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr7:96791000-96798000	Weak transcription	Primary B cells from peripheral blood	blood
35	chr7:96791200-96795600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
36	chr7:96791200-96797000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr7:96791800-96811600	Weak transcription	Adipose Nuclei	Adipose
38	chr7:96793600-96797200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr7:96794000-96796000	Weak transcription	Fetal Intestine Small	intestine
40	chr7:96794200-96796400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr7:96794200-96797000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr7:96794800-96795600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr7:96794800-96795600	Enhancers	Liver	Liver
44	chr7:96795000-96795400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr7:96795000-96795600	ZNF genes & repeats	Primary T cells from cord blood	blood

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