Variant report

Variant	rs1531402
Chromosome Location	chr12:44243739-44243740
allele	A/G
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	chr12:44228652..44231485-chr12:44241299..44244187,4	MCF-7	breast:
3	chr12:44236889..44239645-chr12:44240734..44243980,3	MCF-7	breast:
4	chr12:44228729..44230995-chr12:44242066..44244181,2	K562	blood:

Variant related genes	Relation type
ENSG00000139173	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs11608602	0.85[MEX][hapmap]
rs11835197	0.81[TSI][hapmap]
rs11837742	0.81[TSI][hapmap]
rs13377809	0.87[CEU][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap]
rs17093973	0.83[TSI][hapmap]
rs17535213	1.00[YRI][hapmap]
rs55669442	0.81[EUR][1000 genomes]
rs55821943	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs55913788	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55914098	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs55987826	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs55995646	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56008731	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs56024677	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56066688	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs56134007	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs56168228	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs56312131	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs57066844	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs57331385	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs58531015	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs58824683	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs58938395	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs60120002	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs60221557	0.86[EUR][1000 genomes]
rs60306990	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs60467323	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs60715781	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61930678	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs61930689	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs61930691	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61930693	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61930709	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs61930716	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs61930718	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs61932974	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61933009	0.82[EUR][1000 genomes]
rs7136217	0.83[TSI][hapmap]
rs71435964	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7303909	0.83[TSI][hapmap]
rs73085709	0.82[EUR][1000 genomes]
rs73085734	0.82[EUR][1000 genomes]
rs7971036	0.95[AMR][1000 genomes];1.00[EUR][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:46 , 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	chr12:44230800-44243800	Weak transcription	Ovary	ovary
5	chr12:44230800-44250800	Weak transcription	Pancreas	Pancrea
6	chr12:44230800-44254800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr12:44230800-44260200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr12:44231000-44245800	Weak transcription	Adipose Nuclei	Adipose
9	chr12:44231000-44245800	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr12:44231000-44249800	Weak transcription	Duodenum Mucosa	Duodenum
11	chr12:44231000-44251800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr12:44231000-44252200	Weak transcription	Rectal Smooth Muscle	rectum
13	chr12:44231000-44254600	Weak transcription	GM12878-XiMat	blood
14	chr12:44231200-44261600	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr12:44231400-44245800	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr12:44231400-44245800	Weak transcription	Liver	Liver
17	chr12:44233400-44254400	Weak transcription	Left Ventricle	heart
18	chr12:44233600-44251200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr12:44234200-44254000	Weak transcription	Primary B cells from cord blood	blood
20	chr12:44234600-44260000	Weak transcription	Psoas Muscle	Psoas
21	chr12:44237800-44254200	Weak transcription	Small Intestine	intestine
22	chr12:44238800-44246000	Weak transcription	Primary hematopoietic stem cells	blood
23	chr12:44240400-44245800	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr12:44240400-44293000	Weak transcription	Aorta	Aorta
25	chr12:44241400-44254000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr12:44241600-44245000	Weak transcription	Right Ventricle	heart
27	chr12:44241600-44245000	Weak transcription	HepG2	liver
28	chr12:44241600-44245400	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr12:44241600-44245600	Weak transcription	NH-A	brain
30	chr12:44241600-44245800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr12:44241600-44247000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr12:44241600-44251800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr12:44241600-44252200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr12:44242800-44243800	Weak transcription	Placenta	Placenta
35	chr12:44242800-44244600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr12:44242800-44250800	Weak transcription	Esophagus	oesophagus
37	chr12:44243000-44243800	Weak transcription	Fetal Intestine Large	intestine
38	chr12:44243000-44244200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr12:44243000-44246200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr12:44243000-44247600	Weak transcription	HSMMtube	muscle
41	chr12:44243000-44258000	Weak transcription	Fetal Intestine Small	intestine
42	chr12:44243200-44243800	Weak transcription	HSMM	muscle
43	chr12:44243200-44246400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr12:44243200-44247400	Weak transcription	Hela-S3	cervix
45	chr12:44243200-44252000	Weak transcription	HMEC	breast
46	chr12:44243400-44246200	Weak transcription	NHEK	skin

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