Variant report

Variant	rs3801145
Chromosome Location	chr7:38790947-38790948
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:38777448..38781271-chr7:38790893..38794034,3	K562	blood:
2	chr7:38790727..38792284-chr7:38793430..38795338,2	MCF-7	breast:
3	chr7:38787332..38789165-chr7:38790853..38793676,2	K562	blood:

Extended variants
information (count: 100 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs1017028	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10242048	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10247503	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10251912	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10254567	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10271176	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10486677	0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs10486678	0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs11971020	0.96[ASN][1000 genomes]
rs11979618	0.86[ASN][1000 genomes]
rs11979824	0.96[ASN][1000 genomes]
rs11980882	0.86[CHB][hapmap];0.84[CHD][hapmap];0.85[JPT][hapmap]
rs12533557	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12672237	0.86[ASN][1000 genomes]
rs12672750	0.86[ASN][1000 genomes]
rs12672793	0.86[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs12672885	0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs12674115	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs12701659	0.88[ASN][1000 genomes]
rs1468348	0.91[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs17700072	0.84[ASN][1000 genomes]
rs17700142	0.86[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs17700172	0.91[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs17700190	0.86[ASN][1000 genomes]
rs17700262	0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs17700392	0.96[ASN][1000 genomes]
rs17700752	0.86[CHB][hapmap];0.93[CHD][hapmap];0.83[JPT][hapmap];0.86[ASN][1000 genomes]
rs17767695	0.84[ASN][1000 genomes]
rs17767770	0.88[ASN][1000 genomes]
rs17767818	0.86[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs17768153	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs17768212	0.96[ASN][1000 genomes]
rs17768711	0.89[CHB][hapmap]
rs17768753	0.85[JPT][hapmap]
rs1859494	0.88[ASN][1000 genomes]
rs1859937	0.87[CHB][hapmap];0.90[JPT][hapmap]
rs1978171	0.86[ASN][1000 genomes]
rs1978172	0.86[ASN][1000 genomes]
rs2074655	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs2074657	0.95[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs2107743	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2108507	0.82[CHB][hapmap];0.84[CHD][hapmap];0.85[JPT][hapmap]
rs2189855	0.94[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs2214666	0.96[ASN][1000 genomes]
rs2240351	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2240352	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.83[TSI][hapmap];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2240353	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs2240354	0.95[ASN][1000 genomes]
rs2286082	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2286084	0.96[ASN][1000 genomes]
rs2286086	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs2286087	0.96[ASN][1000 genomes]
rs2286088	0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs2286091	0.96[ASN][1000 genomes]
rs2286094	0.96[ASN][1000 genomes]
rs2286098	0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs2286104	0.96[ASN][1000 genomes]
rs2286105	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs2286106	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.97[TSI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2286109	0.86[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs2392598	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28548028	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34724372	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs35253728	0.88[ASN][1000 genomes]
rs35791079	0.88[ASN][1000 genomes]
rs3735347	0.91[CHB][hapmap];0.95[CHD][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs3801135	0.82[JPT][hapmap]
rs3801139	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.83[TSI][hapmap];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3801140	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.83[TSI][hapmap];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3801141	0.96[ASN][1000 genomes]
rs3801143	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.84[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3801146	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4430003	0.82[JPT][hapmap]
rs4723782	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4723785	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56050717	0.84[ASN][1000 genomes]
rs57091471	0.96[ASN][1000 genomes]
rs60590111	0.86[ASN][1000 genomes]
rs62444078	0.95[ASN][1000 genomes]
rs62444107	0.96[ASN][1000 genomes]
rs6462860	0.86[ASN][1000 genomes]
rs66662538	0.86[ASN][1000 genomes]
rs66796288	0.88[ASN][1000 genomes]
rs66976998	0.83[ASN][1000 genomes]
rs67202646	0.86[ASN][1000 genomes]
rs733150	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73368205	0.93[ASN][1000 genomes]
rs7778570	0.86[ASN][1000 genomes]
rs7779329	0.86[ASN][1000 genomes]
rs7780625	0.82[CHB][hapmap];0.84[CHD][hapmap];0.85[JPT][hapmap]
rs7783546	0.88[ASN][1000 genomes]
rs7783695	0.81[JPT][hapmap]
rs7785911	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.97[TSI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7786389	0.96[ASN][1000 genomes]
rs7788664	0.80[JPT][hapmap]
rs7794030	0.87[ASN][1000 genomes]
rs7795874	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7797871	0.88[ASN][1000 genomes]
rs886646	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv887965	chr7:38706384-38793243	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3801145	EPDR1	cis	cerebellum	SCAN
rs3801145	C7orf10	cis	cerebellum	SCAN
rs3801145	MAB21L2	trans	cerebellum	SCAN
rs3801145	VPS41	cis	multi-tissue	Pritchard
rs3801145	STARD3NL	cis	lymphoblastoid	seeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:38749000-38803600	Weak transcription	Fetal Brain Male	brain
2	chr7:38755000-38791200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr7:38757200-38835400	Weak transcription	Psoas Muscle	Psoas
4	chr7:38759200-38810200	Weak transcription	A549	lung
5	chr7:38759400-38810600	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr7:38760000-38799800	Weak transcription	HUVEC	blood vessel
7	chr7:38760600-38800200	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr7:38761000-38820400	Weak transcription	Stomach Mucosa	stomach
9	chr7:38762600-38793200	Weak transcription	Hela-S3	cervix
10	chr7:38763200-38828000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr7:38763400-38792600	Weak transcription	Small Intestine	intestine
12	chr7:38763400-38828800	Weak transcription	HepG2	liver
13	chr7:38763800-38791600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr7:38765400-38802800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr7:38766000-38791800	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr7:38766600-38791600	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr7:38767200-38792600	Weak transcription	Colonic Mucosa	Colon
18	chr7:38767200-38802800	Weak transcription	Right Ventricle	heart
19	chr7:38767200-38805800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr7:38768400-38791200	Weak transcription	Brain Germinal Matrix	brain
21	chr7:38768400-38791800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr7:38769800-38795000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr7:38774800-38816800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr7:38775600-38791200	Weak transcription	HSMMtube	muscle
25	chr7:38775800-38816600	Strong transcription	Primary monocytes fromperipheralblood	blood
26	chr7:38776400-38792200	Weak transcription	Fetal Heart	heart
27	chr7:38777400-38800400	Strong transcription	Primary B cells from cord blood	blood
28	chr7:38779200-38792800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr7:38779800-38794800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr7:38780000-38792000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
31	chr7:38780800-38792800	Weak transcription	Rectal Smooth Muscle	rectum
32	chr7:38780800-38803600	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr7:38780800-38806000	Weak transcription	Fetal Brain Female	brain
34	chr7:38780800-38828800	Weak transcription	Gastric	stomach
35	chr7:38781400-38805800	Weak transcription	Brain Substantia Nigra	brain
36	chr7:38782200-38791200	Weak transcription	K562	blood
37	chr7:38782600-38791400	Weak transcription	Brain Angular Gyrus	brain
38	chr7:38783000-38791400	Weak transcription	Colon Smooth Muscle	Colon
39	chr7:38783200-38791400	Weak transcription	Ovary	ovary
40	chr7:38784000-38791400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
41	chr7:38784400-38791200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr7:38784400-38805800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr7:38784600-38805800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr7:38784800-38791000	Weak transcription	Fetal Lung	lung
45	chr7:38784800-38791200	Weak transcription	Thymus	Thymus
46	chr7:38784800-38791200	Weak transcription	HSMM	muscle
47	chr7:38784800-38791600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr7:38784800-38835000	Weak transcription	NHEK	skin
49	chr7:38785000-38791200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr7:38785000-38791600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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