Variant report

Variant	rs12989903
Chromosome Location	chr2:153555818-153555819
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:153555340..153556885-chr2:153557265..153559001,2	MCF-7	breast:
2	chr2:153553873..153556846-chr2:153573551..153577346,3	K562	blood:
3	chr2:153553988..153556730-chr2:153566964..153569354,3	K562	blood:
4	chr2:153551426..153554631-chr2:153555293..153557779,3	MCF-7	breast:
5	chr2:153554769..153561611-chr2:153571715..153575304,9	MCF-7	breast:

Variant related genes	Relation type
ENSG00000196504	Chromatin interaction
ENSG00000177917	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10497113	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10931263	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10931271	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10931279	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1135617	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11674911	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11676069	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11694512	0.84[ASN][1000 genomes]
rs11901227	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12475871	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12478681	0.84[ASN][1000 genomes]
rs12693429	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs12990935	1.00[CHB][hapmap]
rs12995388	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12999331	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13003670	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13006652	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13014141	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13017131	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13022436	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13023779	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13023975	0.84[EUR][1000 genomes]
rs1370499	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16831440	0.84[EUR][1000 genomes]
rs16831456	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17328776	1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17400456	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17400938	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17400952	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17400980	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2083097	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2346551	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34199006	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34454505	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34469468	0.84[EUR][1000 genomes]
rs34619076	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34775858	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35002744	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35421285	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35754252	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35894330	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35937874	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs36107565	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36122595	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3811568	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3811569	0.85[CEU][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4575677	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6434172	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66492085	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs66849546	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6728189	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6736003	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs71417232	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs71417235	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72871148	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7591590	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7598878	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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	nsv834421	chr2:153470109-153664235	Strong transcription Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	esv3693438	chr2:153505376-153718246	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:153518800-153558000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr2:153523000-153557800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr2:153523400-153571800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr2:153525000-153557800	Weak transcription	Lung	lung
5	chr2:153525000-153571800	Weak transcription	Small Intestine	intestine
6	chr2:153533200-153558000	Weak transcription	Colonic Mucosa	Colon
7	chr2:153533400-153557800	Weak transcription	Fetal Stomach	stomach
8	chr2:153533400-153558600	Weak transcription	Aorta	Aorta
9	chr2:153533400-153571600	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr2:153533800-153558000	Weak transcription	Stomach Smooth Muscle	stomach
11	chr2:153533800-153572600	Weak transcription	Fetal Brain Male	brain
12	chr2:153536000-153572600	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr2:153537200-153557200	Weak transcription	Thymus	Thymus
14	chr2:153537400-153565400	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr2:153537600-153557400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr2:153537600-153558400	Weak transcription	Fetal Brain Female	brain
17	chr2:153537600-153571800	Weak transcription	Brain Cingulate Gyrus	brain
18	chr2:153537800-153557800	Weak transcription	Brain Germinal Matrix	brain
19	chr2:153539600-153557800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr2:153539600-153557800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr2:153539600-153557800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr2:153539600-153557800	Weak transcription	Esophagus	oesophagus
23	chr2:153539600-153557800	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr2:153539600-153571800	Weak transcription	Brain Anterior Caudate	brain
25	chr2:153539600-153572400	Weak transcription	Brain Angular Gyrus	brain
26	chr2:153539600-153572400	Weak transcription	Pancreas	Pancrea
27	chr2:153541200-153556600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr2:153542000-153557800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr2:153543400-153557800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr2:153544400-153568200	Weak transcription	Fetal Kidney	kidney
31	chr2:153549400-153557800	Weak transcription	Fetal Intestine Small	intestine
32	chr2:153550000-153557600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr2:153550200-153557800	Weak transcription	HMEC	breast
34	chr2:153550400-153557600	Weak transcription	Fetal Lung	lung
35	chr2:153550400-153557800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr2:153550600-153557800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr2:153550600-153558000	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr2:153550800-153557400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr2:153550800-153557600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
40	chr2:153550800-153557800	Weak transcription	Placenta	Placenta
41	chr2:153550800-153558000	Weak transcription	Primary neutrophils fromperipheralblood	blood
42	chr2:153550800-153558000	Weak transcription	Fetal Muscle Trunk	muscle
43	chr2:153551000-153556200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr2:153551000-153558000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
45	chr2:153551200-153557200	Weak transcription	Dnd41	blood
46	chr2:153551200-153557600	Weak transcription	Primary monocytes fromperipheralblood	blood
47	chr2:153551200-153557600	Weak transcription	Primary T cells from cord blood	blood
48	chr2:153551200-153557600	Weak transcription	NHEK	skin
49	chr2:153551200-153557800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr2:153551200-153557800	Weak transcription	Primary B cells from peripheral blood	blood

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