Variant report

Variant	rs7794915
Chromosome Location	chr7:106849393-106849394
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:106849228..106851031-chr7:106852339..106854731,2	MCF-7	breast:
2	chr7:106849189..106851803-chr7:106991183..106993127,2	K562	blood:
3	chr7:106838224..106841860-chr7:106847097..106850411,5	K562	blood:
4	chr7:106812872..106815212-chr7:106848283..106850029,2	K562	blood:
5	chr7:106838412..106842841-chr7:106847097..106851611,6	K562	blood:

Extended variants
information (count: 132 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:129)

rs_ID	r²[population]
rs1002935	1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1018946	0.93[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1018947	0.93[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10487271	0.93[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10953529	0.95[ASN][1000 genomes]
rs10953530	0.93[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10953531	0.93[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10953533	0.93[ASN][1000 genomes]
rs10953534	0.96[ASN][1000 genomes]
rs10953535	0.95[ASN][1000 genomes]
rs10953537	0.90[ASN][1000 genomes]
rs1121312	0.96[ASN][1000 genomes]
rs11761181	0.95[ASN][1000 genomes]
rs11762152	0.84[ASN][1000 genomes]
rs11764448	0.96[ASN][1000 genomes]
rs11766060	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.89[ASN][1000 genomes]
rs11769527	0.96[ASN][1000 genomes]
rs11769861	0.93[ASN][1000 genomes]
rs11769901	0.93[ASN][1000 genomes]
rs11773514	0.92[ASN][1000 genomes]
rs12154285	0.93[ASN][1000 genomes]
rs12531187	0.93[ASN][1000 genomes]
rs12532447	0.93[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12532849	0.93[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs12532953	0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12532967	0.95[ASN][1000 genomes]
rs12533516	0.95[ASN][1000 genomes]
rs12533767	0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12534000	0.93[ASN][1000 genomes]
rs12534676	0.92[ASN][1000 genomes]
rs12535814	0.89[ASN][1000 genomes]
rs12536485	0.95[ASN][1000 genomes]
rs12536491	0.95[ASN][1000 genomes]
rs12536574	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12536603	0.92[ASN][1000 genomes]
rs12537011	0.90[ASN][1000 genomes]
rs12537374	0.92[ASN][1000 genomes]
rs12537730	0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12537733	0.93[ASN][1000 genomes]
rs12540475	0.92[ASN][1000 genomes]
rs1548523	0.92[ASN][1000 genomes]
rs1548524	0.92[ASN][1000 genomes]
rs17349904	0.87[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.92[ASN][1000 genomes]
rs17350182	0.96[ASN][1000 genomes]
rs17425839	1.00[LWK][hapmap]
rs17427123	0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs17427158	0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs17427849	0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs17428071	0.87[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs17428126	0.93[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs17428504	0.96[ASN][1000 genomes]
rs17429118	0.93[ASN][1000 genomes]
rs17429146	0.93[ASN][1000 genomes]
rs1981696	0.93[MEX][hapmap]
rs1989814	0.89[ASN][1000 genomes]
rs2023892	0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2107318	0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2107319	0.87[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2189501	0.95[ASN][1000 genomes]
rs2249043	0.93[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[ASN][1000 genomes]
rs2299422	0.93[ASN][1000 genomes]
rs2395859	0.90[ASN][1000 genomes]
rs257375	0.85[GIH][hapmap]
rs257377	0.92[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap]
rs257387	0.92[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap]
rs2894459	0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];0.93[ASN][1000 genomes]
rs3729876	0.89[GIH][hapmap];1.00[MEX][hapmap]
rs3729877	0.89[GIH][hapmap];0.93[MEX][hapmap]
rs3757713	0.89[ASN][1000 genomes]
rs3779498	0.96[ASN][1000 genomes]
rs3779500	0.85[GIH][hapmap];0.93[MEX][hapmap]
rs3801958	0.92[ASN][1000 genomes]
rs3801959	0.96[ASN][1000 genomes]
rs3801963	0.83[CEU][hapmap];0.93[ASN][1000 genomes]
rs3801965	0.93[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs3815148	0.96[ASN][1000 genomes]
rs3823959	0.90[ASN][1000 genomes]
rs3823960	0.90[ASN][1000 genomes]
rs4727670	0.92[ASN][1000 genomes]
rs4727671	0.93[ASN][1000 genomes]
rs4730222	0.84[ASN][1000 genomes]
rs4730223	0.93[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4730224	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4730226	0.90[ASN][1000 genomes]
rs4730227	0.92[ASN][1000 genomes]
rs4730228	0.95[ASN][1000 genomes]
rs4730229	0.96[ASN][1000 genomes]
rs4730231	0.95[ASN][1000 genomes]
rs4730232	0.95[ASN][1000 genomes]
rs57525841	0.93[ASN][1000 genomes]
rs58319984	0.93[ASN][1000 genomes]
rs58663672	0.95[ASN][1000 genomes]
rs59900773	0.95[ASN][1000 genomes]
rs60255281	0.93[ASN][1000 genomes]
rs61014091	0.84[ASN][1000 genomes]
rs61406169	0.93[ASN][1000 genomes]
rs61511581	0.93[ASN][1000 genomes]
rs61673847	0.93[ASN][1000 genomes]
rs6466162	0.93[ASN][1000 genomes]
rs6946036	0.93[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6946931	0.92[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap]
rs6947675	0.82[CEU][hapmap];0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6949961	0.93[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6951639	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6960813	0.96[ASN][1000 genomes]
rs6963917	0.95[ASN][1000 genomes]
rs6964798	0.95[ASN][1000 genomes]
rs6964966	0.93[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6965001	0.95[ASN][1000 genomes]
rs6967639	0.84[ASN][1000 genomes]
rs6967745	0.93[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6971675	0.93[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6971774	0.93[CHB][hapmap];0.94[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7777976	0.92[ASN][1000 genomes]
rs7779062	0.95[ASN][1000 genomes]
rs7781947	0.93[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7783181	0.95[ASN][1000 genomes]
rs7783562	0.94[ASN][1000 genomes]
rs7789500	0.92[ASN][1000 genomes]
rs7789678	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7793594	0.92[ASN][1000 genomes]
rs7794598	1.00[CHB][hapmap];0.94[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs7794965	0.82[CEU][hapmap];0.93[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7798223	0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7800443	0.96[ASN][1000 genomes]
rs7803290	0.95[ASN][1000 genomes]
rs7981	0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9641378	0.93[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs997311	0.95[ASN][1000 genomes]

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	nsv831087	chr7:106673465-106872460	Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	esv3383027	chr7:106802625-107096474	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv888939	chr7:106849393-107045700	ZNF genes & repeats Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs7794915	COG5	cis	multi-tissue	Pritchard
rs7794915	ATXN7L1	cis	parietal	SCAN
rs7794915	BCAP29	cis	parietal	SCAN
rs7794915	COG5	cis	parietal	SCAN
rs7794915	NRCAM	cis	parietal	SCAN
rs7794915	GPR22	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:106815200-106849400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr7:106817400-106851400	Strong transcription	Primary B cells from peripheral blood	blood
3	chr7:106819600-106851800	Strong transcription	Primary monocytes fromperipheralblood	blood
4	chr7:106819800-106851600	Strong transcription	Dnd41	blood
5	chr7:106820000-106851200	Strong transcription	Primary neutrophils fromperipheralblood	blood
6	chr7:106820000-106851600	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr7:106820200-106851200	Strong transcription	Primary B cells from cord blood	blood
8	chr7:106820200-106851800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr7:106820200-106851800	Strong transcription	Fetal Thymus	thymus
10	chr7:106821000-106854600	Strong transcription	Primary T cells from cord blood	blood
11	chr7:106821200-106851800	Strong transcription	Primary T cells fromperipheralblood	blood
12	chr7:106821200-106851800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr7:106821200-106851800	Strong transcription	Rectal Mucosa Donor 29	rectum
14	chr7:106821400-106851800	Strong transcription	Duodenum Mucosa	Duodenum
15	chr7:106821600-106851600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr7:106821600-106851800	Strong transcription	Primary T helper cells fromperipheralblood	blood
17	chr7:106821800-106851400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr7:106823000-106851200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr7:106823800-106849600	Weak transcription	HMEC	breast
20	chr7:106828600-106849600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr7:106828600-106851800	Strong transcription	Fetal Intestine Large	intestine
22	chr7:106828800-106849800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr7:106828800-106851200	Strong transcription	Primary T helper cells PMA-I stimulated	--
24	chr7:106832000-106852400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr7:106833600-106849400	Weak transcription	Esophagus	oesophagus
26	chr7:106834200-106851600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr7:106834800-106851000	Strong transcription	Thymus	Thymus
28	chr7:106835200-106851800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
29	chr7:106835400-106852200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr7:106835800-106851000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
31	chr7:106835800-106851600	Strong transcription	Fetal Muscle Leg	muscle
32	chr7:106836200-106852000	Strong transcription	Fetal Muscle Trunk	muscle
33	chr7:106836400-106851200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr7:106837000-106851000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr7:106838200-106850600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr7:106838200-106865200	Weak transcription	Stomach Mucosa	stomach
37	chr7:106840000-106853400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr7:106841200-106853000	Weak transcription	Small Intestine	intestine
39	chr7:106841600-106855000	Weak transcription	Pancreatic Islets	Pancreatic Islet
40	chr7:106841800-106851000	Strong transcription	HepG2	liver
41	chr7:106842600-106852000	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr7:106844000-106849800	Weak transcription	Hela-S3	cervix
43	chr7:106844000-106870400	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr7:106844200-106873200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
45	chr7:106844600-106851400	Weak transcription	HUVEC	blood vessel
46	chr7:106844600-106853800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
47	chr7:106844600-106873600	Weak transcription	HUES6 Cell Line	embryonic stem cell
48	chr7:106844600-106880400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
49	chr7:106844600-106888400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr7:106844800-106849800	Weak transcription	H9 Cell Line	embryonic stem cell

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