Variant report

Variant	rs2636290
Chromosome Location	chr1:179096088-179096089
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:179095025..179097028-chr1:179098926..179100910,2	K562	blood:
2	chr1:179075971..179079448-chr1:179095385..179098448,3	MCF-7	breast:

Extended variants
information (count: 67 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs1046385	1.00[ASW][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap]
rs1078872	0.88[GIH][hapmap]
rs10913690	0.88[GIH][hapmap]
rs10913691	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10913697	0.93[GIH][hapmap]
rs1173077	0.95[GIH][hapmap];0.81[JPT][hapmap]
rs12022539	1.00[ASW][hapmap];0.95[CEU][hapmap]
rs12031894	0.87[AFR][1000 genomes]
rs12049237	0.95[CEU][hapmap]
rs12130276	0.93[GIH][hapmap]
rs12402165	0.95[CEU][hapmap]
rs12404921	0.87[AFR][1000 genomes]
rs12408349	1.00[ASW][hapmap];0.95[CEU][hapmap];0.81[CHB][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];0.87[AFR][1000 genomes]
rs1325194	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1475798	1.00[ASW][hapmap];0.89[CEU][hapmap]
rs17362081	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1856968	0.93[GIH][hapmap]
rs2025582	1.00[LWK][hapmap]
rs2050922	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2066162	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2130576	0.93[GIH][hapmap]
rs2171959	0.93[GIH][hapmap]
rs2296377	0.83[AMR][1000 genomes]
rs2493124	0.93[GIH][hapmap]
rs2636266	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.87[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2636274	0.93[GIH][hapmap]
rs2636276	0.88[GIH][hapmap]
rs2636278	1.00[CHB][hapmap];0.97[CHD][hapmap]
rs2636280	0.93[GIH][hapmap]
rs2636287	0.84[JPT][hapmap]
rs2636289	0.87[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs2791941	0.88[GIH][hapmap]
rs2793791	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2793796	0.93[GIH][hapmap]
rs2793797	0.93[GIH][hapmap]
rs2793799	0.95[GIH][hapmap];0.81[JPT][hapmap]
rs2793804	0.87[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2793805	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.87[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs2793807	0.87[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs2793808	0.90[EUR][1000 genomes]
rs2793812	0.90[GIH][hapmap]
rs2793816	0.88[GIH][hapmap]
rs2816179	0.80[EUR][1000 genomes]
rs2816203	0.93[GIH][hapmap]
rs2816209	0.97[GIH][hapmap];0.81[JPT][hapmap]
rs2816213	0.93[GIH][hapmap]
rs3210839	0.92[GIH][hapmap];0.81[JPT][hapmap]
rs380951	0.86[EUR][1000 genomes]
rs3813638	1.00[ASW][hapmap];0.81[MEX][hapmap]
rs3813642	0.88[GIH][hapmap]
rs3813643	0.88[GIH][hapmap]
rs3818433	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs425858	0.86[EUR][1000 genomes]
rs4478776	0.86[EUR][1000 genomes]
rs451088	0.90[GIH][hapmap]
rs4651014	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59777301	0.87[AFR][1000 genomes]
rs61821690	0.87[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs61824368	0.87[AFR][1000 genomes]
rs6425512	1.00[ASW][hapmap];0.81[MEX][hapmap]
rs6675772	0.87[AFR][1000 genomes]
rs7544801	1.00[ASW][hapmap];0.81[MEX][hapmap]
rs915337	0.90[GIH][hapmap]
rs931441	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs9728480	0.93[GIH][hapmap]

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	nsv1012667	chr1:179094571-179120280	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	nsv1002253	chr1:179094571-179120938	Strong transcription Genic enhancers Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2636290	ABL2	cis	parietal	SCAN
rs2636290	TOR3A	cis	Artery Tibial	GTEx
rs2636290	IER5	cis	cerebellum	SCAN
rs2636290	ABL2	cis	cerebellum	SCAN
rs2636290	LHX4	cis	parietal	SCAN
rs2636290	FAM20B	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179059200-179096400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr1:179063200-179112000	Weak transcription	Fetal Kidney	kidney
3	chr1:179064800-179097800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr1:179075400-179096200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
5	chr1:179078600-179097600	Weak transcription	Stomach Mucosa	stomach
6	chr1:179079600-179109800	Weak transcription	Small Intestine	intestine
7	chr1:179080000-179097800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr1:179080000-179097800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr1:179080000-179098600	Weak transcription	Esophagus	oesophagus
10	chr1:179080200-179101600	Weak transcription	Fetal Brain Male	brain
11	chr1:179080400-179103800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr1:179080800-179098400	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr1:179080800-179099000	Weak transcription	Colonic Mucosa	Colon
14	chr1:179080800-179099000	Weak transcription	Spleen	Spleen
15	chr1:179086600-179105000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr1:179086800-179099000	Weak transcription	Right Ventricle	heart
17	chr1:179087800-179097800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr1:179087800-179113000	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr1:179088000-179096400	Weak transcription	Brain Substantia Nigra	brain
20	chr1:179088000-179097800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr1:179088000-179098400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr1:179088000-179098600	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr1:179088000-179099000	Weak transcription	Aorta	Aorta
24	chr1:179088200-179097800	Weak transcription	Primary B cells from cord blood	blood
25	chr1:179088200-179098800	Weak transcription	Brain Hippocampus Middle	brain
26	chr1:179088200-179102400	Weak transcription	Brain Germinal Matrix	brain
27	chr1:179088400-179099200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr1:179088400-179099400	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr1:179088600-179096800	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr1:179088600-179098800	Weak transcription	Ovary	ovary
31	chr1:179088600-179098800	Weak transcription	Rectal Smooth Muscle	rectum
32	chr1:179089000-179097800	Weak transcription	Primary B cells from peripheral blood	blood
33	chr1:179089200-179098400	Weak transcription	Monocytes-CD14+_RO01746	blood
34	chr1:179089200-179099400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr1:179089400-179097600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr1:179089400-179098400	Weak transcription	Primary monocytes fromperipheralblood	blood
37	chr1:179089400-179098400	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr1:179089600-179099000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr1:179090800-179097200	Weak transcription	Primary T helper cells fromperipheralblood	blood
40	chr1:179090800-179097800	Weak transcription	K562	blood
41	chr1:179090800-179098400	Weak transcription	Duodenum Mucosa	Duodenum
42	chr1:179090800-179099200	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr1:179090800-179104400	Weak transcription	Fetal Brain Female	brain
44	chr1:179091000-179097800	Weak transcription	Fetal Thymus	thymus
45	chr1:179091000-179097800	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr1:179091000-179098000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr1:179091000-179098000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr1:179091000-179098200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr1:179091000-179098200	Weak transcription	HepG2	liver
50	chr1:179091000-179098400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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