Variant report

Variant	rs12117159
Chromosome Location	chr1:172324915-172324916
allele	C/G
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	chr1:172319507..172323495-chr1:172324646..172327530,4	MCF-7	breast:
5	chr1:172324502..172327438-chr1:172328565..172330761,2	K562	blood:

Variant related genes	Relation type
ENSG00000252354	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10489284	0.84[CEU][hapmap]
rs10797978	0.84[CEU][hapmap];1.00[ASN][1000 genomes]
rs10797984	0.91[CEU][hapmap];1.00[ASN][1000 genomes]
rs10798029	1.00[ASN][1000 genomes]
rs10911603	0.84[CEU][hapmap];1.00[ASN][1000 genomes]
rs10911624	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs10911627	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10911629	0.82[ASW][hapmap];1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12081260	0.82[CEU][hapmap];1.00[ASN][1000 genomes]
rs12120829	1.00[ASN][1000 genomes]
rs12124608	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12130929	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12132562	1.00[CEU][hapmap];0.82[GIH][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12132925	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12133952	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12134640	1.00[ASN][1000 genomes]
rs12134818	1.00[ASN][1000 genomes]
rs12134821	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12137951	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12140433	1.00[CEU][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12141605	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12142161	0.82[ASW][hapmap];1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12143377	0.89[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12143497	0.82[ASW][hapmap];1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12143622	1.00[CEU][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16844588	1.00[ASN][1000 genomes]
rs17368984	0.82[ASW][hapmap];1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4471302	0.84[CEU][hapmap]
rs59476820	1.00[ASN][1000 genomes]
rs61330781	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6684850	0.87[AMR][1000 genomes]
rs73048544	1.00[ASN][1000 genomes]
rs74126214	0.87[AMR][1000 genomes]
rs9425562	0.84[CEU][hapmap];1.00[ASN][1000 genomes]
rs990363	0.84[CEU][hapmap];0.85[MEX][hapmap];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	chr1:172321200-172325000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
4	chr1:172321200-172325000	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr1:172321200-172326400	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr1:172321200-172327000	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr1:172321200-172327200	Weak transcription	Right Atrium	heart
8	chr1:172321200-172329600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr1:172321400-172325000	Weak transcription	Rectal Smooth Muscle	rectum
10	chr1:172321400-172325200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr1:172321400-172325600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr1:172321400-172326600	Weak transcription	Brain Cingulate Gyrus	brain
13	chr1:172321400-172327000	Weak transcription	Duodenum Mucosa	Duodenum
14	chr1:172321400-172327000	Weak transcription	Small Intestine	intestine
15	chr1:172321400-172327200	Weak transcription	Ovary	ovary
16	chr1:172321600-172325000	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr1:172321600-172327200	Weak transcription	Fetal Heart	heart
18	chr1:172322000-172325200	Weak transcription	HUVEC	blood vessel
19	chr1:172322000-172325600	Weak transcription	NHDF-Ad	bronchial
20	chr1:172322000-172327000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr1:172322000-172327000	Weak transcription	Fetal Stomach	stomach
22	chr1:172322200-172325200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr1:172322200-172325200	Weak transcription	HSMM	muscle
24	chr1:172322200-172325800	Weak transcription	Fetal Lung	lung
25	chr1:172322400-172325000	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr1:172322400-172325000	Weak transcription	Fetal Kidney	kidney
27	chr1:172322400-172325200	Weak transcription	HMEC	breast
28	chr1:172322400-172325400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr1:172322400-172325800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr1:172322400-172326000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr1:172322400-172326000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr1:172322400-172326400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr1:172322400-172327000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr1:172322400-172327000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr1:172322400-172327000	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr1:172322400-172327600	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr1:172322400-172329600	Weak transcription	Gastric	stomach
38	chr1:172322400-172331000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr1:172322600-172325200	Weak transcription	NHEK	skin
40	chr1:172322600-172325800	Weak transcription	NHLF	lung
41	chr1:172322600-172327800	Weak transcription	Psoas Muscle	Psoas
42	chr1:172322600-172328000	Weak transcription	Fetal Muscle Trunk	muscle
43	chr1:172323000-172333000	Enhancers	Fetal Intestine Large	intestine
44	chr1:172323200-172326400	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr1:172323200-172326800	Weak transcription	HUES64 Cell Line	embryonic stem cell
46	chr1:172323400-172325200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr1:172323400-172325200	Enhancers	A549	lung
48	chr1:172323400-172327000	Enhancers	NH-A	brain
49	chr1:172323600-172325200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr1:172323600-172326400	Weak transcription	Primary T helper cells fromperipheralblood	blood

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