Variant report

Variant	rs12987962
Chromosome Location	chr2:190348656-190348657
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:190347309..190351333-chr2:190419513..190421740,3	MCF-7	breast:
2	chr2:190348544..190350498-chr2:190356063..190358536,2	MCF-7	breast:
3	chr2:190304945..190307026-chr2:190347089..190349073,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115368	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10187060	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10497700	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10497703	0.98[ASN][1000 genomes]
rs10755004	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10931414	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10931415	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10931416	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10931418	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10931419	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1112578	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1157910	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11677066	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11688021	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11691691	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs11695159	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12612412	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12613876	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12616234	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12623723	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12988143	0.98[ASN][1000 genomes]
rs12990035	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12990235	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12997620	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13010531	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13015203	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13032853	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13033841	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1356977	0.81[AMR][1000 genomes]
rs1402368	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1520855	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1520857	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1520863	0.82[EUR][1000 genomes]
rs1520864	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1581351	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1949604	0.81[EUR][1000 genomes]
rs1949605	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2119069	0.98[ASN][1000 genomes]
rs2304703	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35997606	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4287797	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4353589	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4666774	0.81[AMR][1000 genomes]
rs4667281	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6728055	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6745108	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7419276	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs744556	0.84[AFR][1000 genomes]
rs7588453	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7593821	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7596592	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs893408	0.84[AFR][1000 genomes]
rs963738	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9679659	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533029	chr2:189812229-190554339	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv875615	chr2:190215527-190444392	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv584062	chr2:190272195-190376493	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:190335000-190348800	Weak transcription	Gastric	stomach
2	chr2:190335000-190351800	Weak transcription	Psoas Muscle	Psoas
3	chr2:190335000-190366200	Weak transcription	Ovary	ovary
4	chr2:190335800-190352600	Weak transcription	Rectal Smooth Muscle	rectum
5	chr2:190336600-190349600	Weak transcription	HSMMtube	muscle
6	chr2:190338600-190349600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr2:190339400-190349400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr2:190339600-190349800	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr2:190339600-190350000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr2:190339600-190352600	Weak transcription	Colon Smooth Muscle	Colon
11	chr2:190340600-190348800	Weak transcription	Stomach Smooth Muscle	stomach
12	chr2:190340800-190352400	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr2:190341600-190350800	Weak transcription	Liver	Liver
14	chr2:190341800-190351000	Weak transcription	HMEC	breast
15	chr2:190341800-190351200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr2:190342400-190357000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr2:190342600-190349000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr2:190342800-190350000	Weak transcription	HSMM	muscle
19	chr2:190346200-190349600	Enhancers	Placenta	Placenta
20	chr2:190348000-190350000	Enhancers	Skeletal Muscle Female	skeletal muscle
21	chr2:190348200-190350000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr2:190348400-190348800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr2:190348400-190348800	Enhancers	Spleen	Spleen
24	chr2:190348600-190348800	Enhancers	H1 Cell Line	embryonic stem cell
25	chr2:190348600-190348800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr2:190348600-190348800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
27	chr2:190348600-190348800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
28	chr2:190348600-190348800	Enhancers	Right Ventricle	heart
29	chr2:190348600-190349000	Enhancers	Left Ventricle	heart
30	chr2:190348600-190349000	Enhancers	Pancreas	Pancrea
31	chr2:190348600-190349000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
32	chr2:190348600-190349200	Enhancers	Fetal Intestine Large	intestine
33	chr2:190348600-190349200	Enhancers	Fetal Intestine Small	intestine

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