Variant report

Variant	rs2286106
Chromosome Location	chr7:38778411-38778412
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	chr7:38777448..38781271-chr7:38790893..38794034,3	K562	blood:
2	chr7:38776633..38779094-chr7:38783053..38785057,2	K562	blood:

Extended variants
information (count: 101 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs1017028	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10242048	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10247503	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10251912	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10254567	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10271176	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10486677	0.95[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs10486678	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs11971020	0.99[ASN][1000 genomes]
rs11979618	0.88[ASN][1000 genomes]
rs11979824	0.99[ASN][1000 genomes]
rs11980882	0.86[CHB][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap]
rs12533557	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12672237	0.88[ASN][1000 genomes]
rs12672750	0.88[ASN][1000 genomes]
rs12672793	0.86[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs12672885	0.95[CHB][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs12674115	0.82[CHB][hapmap];0.80[JPT][hapmap]
rs12701659	0.90[ASN][1000 genomes]
rs1468348	0.91[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs17700072	0.86[ASN][1000 genomes]
rs17700142	0.86[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs17700172	0.91[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs17700190	0.88[ASN][1000 genomes]
rs17700262	0.95[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs17700392	0.99[ASN][1000 genomes]
rs17700752	0.86[CHB][hapmap];0.95[CHD][hapmap];0.83[JPT][hapmap];0.88[ASN][1000 genomes]
rs17767695	0.86[ASN][1000 genomes]
rs17767770	0.90[ASN][1000 genomes]
rs17767818	0.86[CHB][hapmap];0.91[CHD][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs17768153	0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs17768212	0.99[ASN][1000 genomes]
rs17768711	0.89[CHB][hapmap]
rs17768753	0.85[JPT][hapmap]
rs1859494	0.90[ASN][1000 genomes]
rs1859937	0.87[CHB][hapmap];0.90[JPT][hapmap]
rs1864886	0.80[JPT][hapmap]
rs1978171	0.88[ASN][1000 genomes]
rs1978172	0.88[ASN][1000 genomes]
rs2074655	0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs2074657	0.95[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];0.96[ASN][1000 genomes]
rs2107743	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2108507	0.82[CHB][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap]
rs2189855	0.94[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs2214666	0.99[ASN][1000 genomes]
rs2240351	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2240352	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.87[TSI][hapmap];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2240353	0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs2240354	0.97[ASN][1000 genomes]
rs2286082	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2286084	0.99[ASN][1000 genomes]
rs2286086	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2286087	0.99[ASN][1000 genomes]
rs2286088	0.95[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs2286091	0.99[ASN][1000 genomes]
rs2286094	0.98[ASN][1000 genomes]
rs2286098	0.95[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs2286104	0.99[ASN][1000 genomes]
rs2286105	0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs2286109	0.86[CHB][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs2392598	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28548028	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34724372	0.86[CHB][hapmap];0.80[JPT][hapmap]
rs35253728	0.90[ASN][1000 genomes]
rs35791079	0.90[ASN][1000 genomes]
rs3735347	0.91[CHB][hapmap];0.93[CHD][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs3801135	0.81[JPT][hapmap]
rs3801139	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.87[TSI][hapmap];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3801140	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.84[MKK][hapmap];0.87[TSI][hapmap];0.89[YRI][hapmap];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3801141	0.99[ASN][1000 genomes]
rs3801143	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.89[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3801145	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]
rs3801146	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4430003	0.81[JPT][hapmap]
rs4723782	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4723785	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56002981	0.80[ASN][1000 genomes]
rs56050717	0.86[ASN][1000 genomes]
rs57091471	0.99[ASN][1000 genomes]
rs60590111	0.88[ASN][1000 genomes]
rs62444078	0.97[ASN][1000 genomes]
rs62444107	0.99[ASN][1000 genomes]
rs6462860	0.88[ASN][1000 genomes]
rs66662538	0.88[ASN][1000 genomes]
rs66796288	0.90[ASN][1000 genomes]
rs66976998	0.85[ASN][1000 genomes]
rs67202646	0.88[ASN][1000 genomes]
rs733150	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73368205	0.95[ASN][1000 genomes]
rs7778570	0.88[ASN][1000 genomes]
rs7779329	0.88[ASN][1000 genomes]
rs7780625	0.82[CHB][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap]
rs7783546	0.90[ASN][1000 genomes]
rs7783695	0.85[JPT][hapmap]
rs7785911	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[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];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7786389	0.99[ASN][1000 genomes]
rs7794030	0.89[ASN][1000 genomes]
rs7795874	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.94[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7797871	0.90[ASN][1000 genomes]
rs886646	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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
rs2286106	EPDR1	cis	cerebellum	SCAN
rs2286106	MAB21L2	trans	cerebellum	SCAN
rs2286106	STARD3NL	cis	lymphoblastoid	seeQTL
rs2286106	C7orf10	cis	cerebellum	SCAN
rs2286106	VPS41	cis	multi-tissue	Pritchard

Chromatin state (count:121 , 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	chr7:38757000-38784200	Weak transcription	HMEC	breast
4	chr7:38757200-38835400	Weak transcription	Psoas Muscle	Psoas
5	chr7:38758600-38780600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr7:38758800-38780000	Weak transcription	Brain Substantia Nigra	brain
7	chr7:38759200-38810200	Weak transcription	A549	lung
8	chr7:38759400-38810600	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr7:38759600-38779600	Weak transcription	Thymus	Thymus
10	chr7:38759600-38784200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr7:38759800-38780600	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr7:38760000-38799800	Weak transcription	HUVEC	blood vessel
13	chr7:38760600-38800200	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr7:38761000-38820400	Weak transcription	Stomach Mucosa	stomach
15	chr7:38761200-38785400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr7:38762600-38793200	Weak transcription	Hela-S3	cervix
17	chr7:38763200-38828000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr7:38763400-38780400	Weak transcription	Fetal Kidney	kidney
19	chr7:38763400-38792600	Weak transcription	Small Intestine	intestine
20	chr7:38763400-38828800	Weak transcription	HepG2	liver
21	chr7:38763800-38791600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr7:38764400-38787600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr7:38764800-38784200	Weak transcription	NHEK	skin
24	chr7:38765400-38784200	Weak transcription	NHLF	lung
25	chr7:38765400-38789600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr7:38765400-38802800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr7:38765600-38779600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr7:38765600-38779600	Weak transcription	Spleen	Spleen
29	chr7:38765600-38784200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr7:38765600-38784400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr7:38766000-38784200	Weak transcription	NH-A	brain
32	chr7:38766000-38791800	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr7:38766200-38780000	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr7:38766200-38783400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr7:38766600-38780600	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr7:38766600-38782600	Weak transcription	Colon Smooth Muscle	Colon
37	chr7:38766600-38791600	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr7:38766800-38784200	Weak transcription	NHDF-Ad	bronchial
39	chr7:38767000-38779200	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr7:38767200-38779800	Weak transcription	Primary T helper cells PMA-I stimulated	--
41	chr7:38767200-38779800	Weak transcription	Rectal Smooth Muscle	rectum
42	chr7:38767200-38780200	Weak transcription	Ovary	ovary
43	chr7:38767200-38780400	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr7:38767200-38792600	Weak transcription	Colonic Mucosa	Colon
45	chr7:38767200-38802800	Weak transcription	Right Ventricle	heart
46	chr7:38767200-38805800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr7:38767400-38779600	Weak transcription	Dnd41	blood
48	chr7:38767600-38780400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr7:38767800-38780200	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr7:38768000-38779000	Weak transcription	Brain Inferior Temporal Lobe	brain

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