Variant report

Variant	rs990363
Chromosome Location	chr1:172325029-172325030
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:172315289..172319406-chr1:172322030..172325808,4	MCF-7	breast:
2	chr1:172322016..172323683-chr1:172323746..172325652,2	MCF-7	breast:
3	chr1:172075448..172077009-chr1:172323727..172325300,2	MCF-7	breast:
4	chr1:171972033..171974516-chr1:172324931..172327450,2	MCF-7	breast:
5	chr1:172319507..172323495-chr1:172324646..172327530,4	MCF-7	breast:
6	chr1:172324502..172327438-chr1:172328565..172330761,2	K562	blood:

Variant related genes	Relation type
ENSG00000252354	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10489284	0.84[CEU][hapmap]
rs10797978	1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];0.85[MKK][hapmap];0.89[TSI][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10797984	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10798029	1.00[ASN][1000 genomes]
rs10911603	1.00[CEU][hapmap];0.90[GIH][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10911624	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10911627	1.00[ASN][1000 genomes]
rs10911629	0.84[CEU][hapmap];0.85[GIH][hapmap];0.85[MEX][hapmap];0.84[TSI][hapmap];1.00[ASN][1000 genomes]
rs12081260	1.00[CEU][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12117159	0.84[CEU][hapmap];0.85[MEX][hapmap];1.00[ASN][1000 genomes]
rs12120829	1.00[ASN][1000 genomes]
rs12124608	1.00[ASN][1000 genomes]
rs12130929	1.00[ASN][1000 genomes]
rs12132562	0.84[CEU][hapmap];0.85[MEX][hapmap];1.00[ASN][1000 genomes]
rs12132925	0.84[CEU][hapmap];1.00[ASN][1000 genomes]
rs12133952	0.84[CEU][hapmap];1.00[ASN][1000 genomes]
rs12134640	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12134818	1.00[ASN][1000 genomes]
rs12134821	0.84[CEU][hapmap];1.00[ASN][1000 genomes]
rs12137951	0.84[CEU][hapmap];1.00[ASN][1000 genomes]
rs12140433	0.83[CEU][hapmap];1.00[ASN][1000 genomes]
rs12141605	1.00[ASN][1000 genomes]
rs12142161	0.84[CEU][hapmap];0.85[GIH][hapmap];0.85[MEX][hapmap];0.84[TSI][hapmap]
rs12143377	1.00[ASN][1000 genomes]
rs12143497	0.84[CEU][hapmap];0.85[GIH][hapmap];0.85[MEX][hapmap];0.84[TSI][hapmap];1.00[ASN][1000 genomes]
rs12143622	0.84[CEU][hapmap];1.00[ASN][1000 genomes]
rs16844588	1.00[ASN][1000 genomes]
rs17368984	0.84[CEU][hapmap];0.85[GIH][hapmap];0.85[MEX][hapmap];0.84[TSI][hapmap];1.00[ASN][1000 genomes]
rs4471302	0.84[CEU][hapmap]
rs59469921	0.90[EUR][1000 genomes]
rs59476820	1.00[ASN][1000 genomes]
rs61330781	1.00[ASN][1000 genomes]
rs73048544	1.00[ASN][1000 genomes]
rs9425562	1.00[CEU][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.91[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	nsv3543	chr1:172323563-172334586	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:172313400-172327000	Weak transcription	Aorta	Aorta
2	chr1:172320800-172332800	Enhancers	Fetal Intestine Small	intestine
3	chr1:172321200-172326400	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr1:172321200-172327000	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr1:172321200-172327200	Weak transcription	Right Atrium	heart
6	chr1:172321200-172329600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr1:172321400-172325200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr1:172321400-172325600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr1:172321400-172326600	Weak transcription	Brain Cingulate Gyrus	brain
10	chr1:172321400-172327000	Weak transcription	Duodenum Mucosa	Duodenum
11	chr1:172321400-172327000	Weak transcription	Small Intestine	intestine
12	chr1:172321400-172327200	Weak transcription	Ovary	ovary
13	chr1:172321600-172327200	Weak transcription	Fetal Heart	heart
14	chr1:172322000-172325200	Weak transcription	HUVEC	blood vessel
15	chr1:172322000-172325600	Weak transcription	NHDF-Ad	bronchial
16	chr1:172322000-172327000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr1:172322000-172327000	Weak transcription	Fetal Stomach	stomach
18	chr1:172322200-172325200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr1:172322200-172325200	Weak transcription	HSMM	muscle
20	chr1:172322200-172325800	Weak transcription	Fetal Lung	lung
21	chr1:172322400-172325200	Weak transcription	HMEC	breast
22	chr1:172322400-172325400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr1:172322400-172325800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr1:172322400-172326000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr1:172322400-172326000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr1:172322400-172326400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr1:172322400-172327000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr1:172322400-172327000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr1:172322400-172327000	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr1:172322400-172327600	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr1:172322400-172329600	Weak transcription	Gastric	stomach
32	chr1:172322400-172331000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr1:172322600-172325200	Weak transcription	NHEK	skin
34	chr1:172322600-172325800	Weak transcription	NHLF	lung
35	chr1:172322600-172327800	Weak transcription	Psoas Muscle	Psoas
36	chr1:172322600-172328000	Weak transcription	Fetal Muscle Trunk	muscle
37	chr1:172323000-172333000	Enhancers	Fetal Intestine Large	intestine
38	chr1:172323200-172326400	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr1:172323200-172326800	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr1:172323400-172325200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr1:172323400-172325200	Enhancers	A549	lung
42	chr1:172323400-172327000	Enhancers	NH-A	brain
43	chr1:172323600-172325200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr1:172323600-172326400	Weak transcription	Primary T helper cells fromperipheralblood	blood
45	chr1:172323600-172328200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
46	chr1:172323800-172325800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr1:172323800-172326800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
48	chr1:172324000-172325800	Weak transcription	Primary T helper cells PMA-I stimulated	--
49	chr1:172324000-172326200	Weak transcription	Stomach Mucosa	stomach
50	chr1:172324000-172326400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

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