Variant report

Variant	rs12298970
Chromosome Location	chr12:44237256-44237257
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:44235291..44238339-chr12:44243528..44246812,3	K562	blood:
2	chr12:44236123..44237958-chr12:44238199..44240039,2	MCF-7	breast:
3	chr12:44195094..44197185-chr12:44236657..44238234,2	MCF-7	breast:
4	chr12:44228890..44231522-chr12:44236101..44238646,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000139173	Chromatin interaction

Extended variants
information (count: 101 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs1057486	0.95[EUR][1000 genomes]
rs10748373	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10748378	0.83[EUR][1000 genomes]
rs10785462	0.83[EUR][1000 genomes]
rs10785463	0.83[EUR][1000 genomes]
rs10785466	0.83[EUR][1000 genomes]
rs10880578	0.85[EUR][1000 genomes]
rs10880585	0.83[EUR][1000 genomes]
rs11182293	0.94[EUR][1000 genomes]
rs11182324	0.83[EUR][1000 genomes]
rs11182325	0.83[EUR][1000 genomes]
rs12311962	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12314126	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1358705	0.85[EUR][1000 genomes]
rs1406787	0.90[EUR][1000 genomes]
rs1609548	0.83[EUR][1000 genomes]
rs1609549	0.83[EUR][1000 genomes]
rs1610291	0.83[EUR][1000 genomes]
rs1614042	0.85[EUR][1000 genomes]
rs1621279	0.95[EUR][1000 genomes]
rs1622590	0.85[EUR][1000 genomes]
rs1623667	0.84[EUR][1000 genomes]
rs1623829	0.92[EUR][1000 genomes]
rs1675755	0.82[EUR][1000 genomes]
rs1675756	0.87[EUR][1000 genomes]
rs1675758	0.87[EUR][1000 genomes]
rs1675764	0.85[EUR][1000 genomes]
rs1675765	0.95[EUR][1000 genomes]
rs1675766	0.88[ASN][1000 genomes]
rs1675767	0.93[EUR][1000 genomes]
rs1675769	0.95[EUR][1000 genomes]
rs1675771	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1675774	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1675776	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1675777	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1675778	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1675781	0.83[EUR][1000 genomes]
rs1675782	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1675783	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1675784	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1675785	0.82[EUR][1000 genomes]
rs1675786	1.00[ASN][1000 genomes]
rs1675787	0.85[EUR][1000 genomes]
rs1675788	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1675789	0.85[EUR][1000 genomes]
rs1675790	0.85[EUR][1000 genomes]
rs1675791	1.00[ASN][1000 genomes]
rs1731422	0.88[ASN][1000 genomes]
rs1731423	0.89[EUR][1000 genomes]
rs1731425	0.80[ASN][1000 genomes]
rs1731430	0.86[EUR][1000 genomes]
rs1731431	0.87[EUR][1000 genomes]
rs1731432	0.87[EUR][1000 genomes]
rs1731434	0.90[EUR][1000 genomes]
rs1731438	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1731439	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1731440	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1731442	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1731448	0.98[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs1731449	0.88[ASN][1000 genomes]
rs1731452	0.95[EUR][1000 genomes]
rs1731453	0.88[ASN][1000 genomes]
rs1731454	0.95[EUR][1000 genomes]
rs1731456	0.85[EUR][1000 genomes]
rs1731457	0.83[EUR][1000 genomes]
rs1731458	0.85[EUR][1000 genomes]
rs1731459	0.85[EUR][1000 genomes]
rs2219629	0.93[EUR][1000 genomes]
rs2407783	0.83[EUR][1000 genomes]
rs2447113	0.87[EUR][1000 genomes]
rs2447114	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2447115	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2447116	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2699992	0.88[ASN][1000 genomes]
rs2951435	0.85[EUR][1000 genomes]
rs2951436	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4238089	0.83[EUR][1000 genomes]
rs4238091	0.83[EUR][1000 genomes]
rs4363674	0.83[EUR][1000 genomes]
rs4469953	0.83[EUR][1000 genomes]
rs4537822	0.83[EUR][1000 genomes]
rs4572198	0.83[EUR][1000 genomes]
rs4572199	0.83[EUR][1000 genomes]
rs4609659	0.83[EUR][1000 genomes]
rs4768049	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4768053	0.81[EUR][1000 genomes]
rs4768538	0.83[EUR][1000 genomes]
rs4768543	0.81[EUR][1000 genomes]
rs5019975	0.83[EUR][1000 genomes]
rs7295151	0.81[EUR][1000 genomes]
rs7305609	0.97[EUR][1000 genomes]
rs73096934	0.97[EUR][1000 genomes]
rs73098836	1.00[ASN][1000 genomes]
rs7953229	0.88[ASN][1000 genomes]
rs7955615	0.83[EUR][1000 genomes]
rs7957146	0.94[ASN][1000 genomes]
rs7958314	0.94[ASN][1000 genomes]
rs7965635	0.88[ASN][1000 genomes]
rs7966024	0.94[ASN][1000 genomes]

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	nsv933142	chr12:44130156-44278300	Active TSS Flanking Active TSS Genic enhancers Weak transcription Strong transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv899048	chr12:44209423-44307888	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:44230400-44243800	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr12:44230400-44244200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr12:44230400-44250800	Weak transcription	Gastric	stomach
4	chr12:44230600-44241200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr12:44230800-44241200	Weak transcription	Placenta	Placenta
6	chr12:44230800-44243800	Weak transcription	Ovary	ovary
7	chr12:44230800-44250800	Weak transcription	Pancreas	Pancrea
8	chr12:44230800-44254800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr12:44230800-44260200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr12:44231000-44239200	Weak transcription	Stomach Smooth Muscle	stomach
11	chr12:44231000-44240200	Weak transcription	Hela-S3	cervix
12	chr12:44231000-44240800	Weak transcription	Primary B cells from peripheral blood	blood
13	chr12:44231000-44241200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr12:44231000-44242800	Weak transcription	Colon Smooth Muscle	Colon
15	chr12:44231000-44245800	Weak transcription	Adipose Nuclei	Adipose
16	chr12:44231000-44245800	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr12:44231000-44249800	Weak transcription	Duodenum Mucosa	Duodenum
18	chr12:44231000-44251800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr12:44231000-44252200	Weak transcription	Rectal Smooth Muscle	rectum
20	chr12:44231000-44254600	Weak transcription	GM12878-XiMat	blood
21	chr12:44231200-44238000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr12:44231200-44238400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr12:44231200-44238600	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr12:44231200-44261600	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr12:44231400-44245800	Weak transcription	Primary T cells fromperipheralblood	blood
26	chr12:44231400-44245800	Weak transcription	Liver	Liver
27	chr12:44231800-44241000	Weak transcription	Fetal Intestine Small	intestine
28	chr12:44232200-44238600	Weak transcription	Fetal Intestine Large	intestine
29	chr12:44232200-44239600	Weak transcription	Brain Angular Gyrus	brain
30	chr12:44232200-44240200	Weak transcription	HMEC	breast
31	chr12:44233400-44254400	Weak transcription	Left Ventricle	heart
32	chr12:44233600-44251200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr12:44234200-44254000	Weak transcription	Primary B cells from cord blood	blood
34	chr12:44234400-44238400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr12:44234600-44260000	Weak transcription	Psoas Muscle	Psoas
36	chr12:44235200-44238400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr12:44235600-44241200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr12:44235800-44240800	Weak transcription	HSMM	muscle
39	chr12:44235800-44241200	Weak transcription	NHDF-Ad	bronchial
40	chr12:44236000-44237800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr12:44236000-44240800	Weak transcription	HSMMtube	muscle
42	chr12:44236000-44241000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr12:44236200-44241000	Weak transcription	Osteobl	bone
44	chr12:44236200-44241200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr12:44236400-44241200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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