Variant report

Variant	rs16949946
Chromosome Location	chr12:120537273-120537274
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:120534696..120538363-chr12:120637562..120639888,4	K562	blood:
2	chr12:120534696..120538363-chr12:120637562..120641387,4	K562	blood:
3	chr12:120537048..120541245-chr12:120553607..120557723,6	MCF-7	breast:
4	chr12:120426493..120428297-chr12:120534910..120538709,3	MCF-7	breast:
5	chr12:120537177..120551260-chr12:120551865..120557471,32	MCF-7	breast:
6	chr12:120534104..120540073-chr12:120552292..120555790,7	K562	blood:
7	chr12:120515805..120518721-chr12:120536191..120539691,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000111737	Chromatin interaction
ENSG00000089157	Chromatin interaction
ENSG00000135127	Chromatin interaction
ENSG00000255857	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10128766	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];0.85[JPT][hapmap];0.87[LWK][hapmap];0.84[MEX][hapmap];0.87[MKK][hapmap];0.94[TSI][hapmap];0.87[YRI][hapmap];0.82[ASN][1000 genomes]
rs10400498	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];0.84[MEX][hapmap];0.87[MKK][hapmap];0.94[TSI][hapmap];0.87[YRI][hapmap];0.81[AFR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10400560	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10849731	0.82[ASN][1000 genomes]
rs10849732	0.86[CHB][hapmap];0.89[CHD][hapmap];0.90[GIH][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs10849735	0.86[CHB][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs10849736	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];0.84[MEX][hapmap];0.87[MKK][hapmap];0.88[TSI][hapmap];0.87[YRI][hapmap];0.88[ASN][1000 genomes]
rs11064987	0.80[ASN][1000 genomes]
rs11064988	0.81[ASN][1000 genomes]
rs11064996	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11065003	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.83[MKK][hapmap];0.87[TSI][hapmap];0.87[YRI][hapmap];0.88[ASN][1000 genomes]
rs11833221	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12310269	0.83[ASN][1000 genomes]
rs12310591	0.88[ASN][1000 genomes]
rs12313413	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12318774	0.82[ASN][1000 genomes]
rs12320793	0.80[ASN][1000 genomes]
rs12322236	0.82[ASN][1000 genomes]
rs12422923	0.88[ASN][1000 genomes]
rs16949901	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16949961	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17841967	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2239200	0.86[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2239201	0.86[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.87[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2239202	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2239203	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2239204	0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2240311	0.82[CHB][hapmap]
rs2283359	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2283360	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2283361	0.81[ASN][1000 genomes]
rs2286040	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.92[MKK][hapmap];0.94[TSI][hapmap];0.87[YRI][hapmap];0.82[AFR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28726166	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4767869	0.82[ASN][1000 genomes]
rs4767871	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4767872	0.88[ASN][1000 genomes]
rs4767875	0.88[ASN][1000 genomes]
rs4767876	0.91[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.81[AFR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58272825	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59168361	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60466490	0.88[ASN][1000 genomes]
rs6490281	0.82[CHB][hapmap]
rs7298183	0.82[ASN][1000 genomes]
rs7298727	0.82[ASN][1000 genomes]
rs7300023	0.86[ASW][hapmap];0.86[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.94[TSI][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7312971	0.86[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs7397339	0.88[ASN][1000 genomes]
rs7958402	0.82[ASN][1000 genomes]
rs7958497	1.00[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];0.88[TSI][hapmap];0.80[ASN][1000 genomes]
rs7965829	1.00[ASW][hapmap];0.87[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];0.84[MEX][hapmap];0.80[MKK][hapmap];0.94[TSI][hapmap];0.81[YRI][hapmap];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7968557	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.87[YRI][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7971249	0.83[CHB][hapmap]
rs7978927	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3525916	chr12:120345352-120665045	Bivalent Enhancer Genic enhancers Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
2	esv3525917	chr12:120345352-120665045	Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
3	nsv899555	chr12:120519124-120840522	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	499 gene(s)	inside rSNPs	diseases
4	nsv519657	chr12:120533696-120676090	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
5	nsv560433	chr12:120533696-120676090	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
6	nsv560434	chr12:120534147-120545718	Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:120525600-120539200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr12:120525600-120551800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr12:120525800-120539200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr12:120525800-120553400	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr12:120527400-120546800	Strong transcription	Thymus	Thymus
6	chr12:120527600-120537600	Strong transcription	Primary T helper cells PMA-I stimulated	--
7	chr12:120527600-120538800	Strong transcription	Primary T helper cells fromperipheralblood	blood
8	chr12:120527600-120539200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr12:120527600-120539800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr12:120527600-120540400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr12:120527600-120546000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr12:120528400-120537400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr12:120528600-120537400	Strong transcription	Gastric	stomach
14	chr12:120528600-120537800	Strong transcription	Pancreas	Pancrea
15	chr12:120528600-120538400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr12:120528600-120538800	Strong transcription	NHEK	skin
17	chr12:120529000-120540400	Strong transcription	Primary neutrophils fromperipheralblood	blood
18	chr12:120529000-120546800	Strong transcription	Dnd41	blood
19	chr12:120529200-120537800	Strong transcription	Muscle Satellite Cultured Cells	--
20	chr12:120529400-120538400	Strong transcription	Lung	lung
21	chr12:120529400-120538400	Strong transcription	NHLF	lung
22	chr12:120529600-120538200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
23	chr12:120529600-120538200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr12:120529600-120538200	Weak transcription	Psoas Muscle	Psoas
25	chr12:120529600-120543000	Strong transcription	Sigmoid Colon	Sigmoid Colon
26	chr12:120529800-120539200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr12:120529800-120542200	Strong transcription	Fetal Intestine Large	intestine
28	chr12:120530000-120539200	Strong transcription	Primary B cells from peripheral blood	blood
29	chr12:120530400-120538400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr12:120530800-120540400	Strong transcription	Primary monocytes fromperipheralblood	blood
31	chr12:120531600-120537600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr12:120531800-120538400	Strong transcription	Rectal Mucosa Donor 29	rectum
33	chr12:120532000-120537800	Strong transcription	Placenta	Placenta
34	chr12:120532200-120539000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr12:120532200-120539600	Strong transcription	Primary T cells from cord blood	blood
36	chr12:120532400-120537600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr12:120532400-120538000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
38	chr12:120532400-120538000	Strong transcription	Brain Germinal Matrix	brain
39	chr12:120532400-120538000	Strong transcription	Duodenum Mucosa	Duodenum
40	chr12:120532400-120538400	Strong transcription	Placenta Amnion	Placenta Amnion
41	chr12:120532400-120539000	Strong transcription	Rectal Mucosa Donor 31	rectum
42	chr12:120532400-120539800	Strong transcription	Monocytes-CD14+_RO01746	blood
43	chr12:120532600-120538000	Strong transcription	Duodenum Smooth Muscle	Duodenum
44	chr12:120532600-120538000	Weak transcription	Fetal Heart	heart
45	chr12:120532600-120539000	Strong transcription	GM12878-XiMat	blood
46	chr12:120532600-120539200	Strong transcription	Fetal Intestine Small	intestine
47	chr12:120532600-120539400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr12:120532600-120539400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr12:120532600-120539600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr12:120532800-120537800	Strong transcription	Spleen	Spleen

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