Variant report

Variant	rs13411660
Chromosome Location	chr2:234208258-234208259
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:234196980..234199300-chr2:234206108..234208506,2	MCF-7	breast:
2	chr2:234206531..234209535-chr2:234260932..234264181,3	MCF-7	breast:
3	chr2:234201699..234203441-chr2:234207264..234209148,2	K562	blood:

Variant related genes	Relation type
ENSG00000251791	Chromatin interaction
ENSG00000259793	Chromatin interaction
ENSG00000077044	Chromatin interaction
ENSG00000243637	Chromatin interaction
ENSG00000085978	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10164737	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10165561	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10167613	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10178603	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10186850	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10187752	0.88[ASN][1000 genomes]
rs10187822	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10192702	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10195395	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10196794	0.82[AFR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10199278	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10203952	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10206299	0.91[ASN][1000 genomes]
rs10210302	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1045100	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10929322	0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs10929325	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10929326	0.81[EUR][1000 genomes]
rs11679791	0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11680089	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11680130	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11687982	0.85[ASN][1000 genomes]
rs11688431	0.88[ASN][1000 genomes]
rs11690131	0.87[ASN][1000 genomes]
rs11694081	0.86[ASN][1000 genomes]
rs11893210	0.81[ASN][1000 genomes]
rs12162308	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12692254	0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12994971	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12994997	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13003866	0.91[ASN][1000 genomes]
rs13009506	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13015823	0.83[JPT][hapmap]
rs13035837	0.83[JPT][hapmap]
rs13391356	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13418066	0.91[ASN][1000 genomes]
rs1441092	0.83[JPT][hapmap]
rs1596017	0.89[ASN][1000 genomes]
rs2119505	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2241878	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2241879	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2241880	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2289472	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2289474	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2289477	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs28454240	0.91[ASN][1000 genomes]
rs2880080	0.86[CEU][hapmap];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34123137	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34701569	0.90[ASN][1000 genomes]
rs35300242	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs36001488	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3792104	0.80[YRI][hapmap]
rs3792106	0.95[CHB][hapmap];0.84[ASN][1000 genomes]
rs3792108	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3792109	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3792111	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3792112	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3816234	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3828309	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55835501	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56049444	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56227616	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6431654	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6431660	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6431661	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6705964	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6708373	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6738490	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6745825	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6752107	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7559194	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.96[AMR][1000 genomes];0.98[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	nsv584699	chr2:234182240-234255547	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv584700	chr2:234199401-234364426	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234181400-234216400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr2:234199200-234210200	Weak transcription	Stomach Mucosa	stomach
3	chr2:234203200-234209000	Weak transcription	Fetal Brain Male	brain
4	chr2:234203400-234209800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr2:234203400-234216000	Weak transcription	Hela-S3	cervix
6	chr2:234204000-234211000	Weak transcription	Fetal Lung	lung
7	chr2:234204800-234208800	Weak transcription	Placenta	Placenta
8	chr2:234204800-234209400	Weak transcription	NHLF	lung
9	chr2:234204800-234210400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr2:234205000-234209000	Weak transcription	GM12878-XiMat	blood
11	chr2:234205000-234216200	Weak transcription	Left Ventricle	heart
12	chr2:234205200-234208400	Weak transcription	Gastric	stomach
13	chr2:234205200-234208600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr2:234205200-234209000	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr2:234205200-234209200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr2:234205200-234210400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr2:234205200-234211600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr2:234205200-234211800	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr2:234205400-234209200	Weak transcription	Brain Cingulate Gyrus	brain
20	chr2:234205400-234209400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr2:234205400-234209600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr2:234205400-234211800	Weak transcription	Stomach Smooth Muscle	stomach
23	chr2:234205400-234213400	Weak transcription	Lung	lung
24	chr2:234205400-234219800	Weak transcription	Spleen	Spleen
25	chr2:234205600-234208400	Weak transcription	Primary neutrophils fromperipheralblood	blood
26	chr2:234205600-234209000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr2:234206000-234208800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr2:234206000-234214800	Weak transcription	Pancreas	Pancrea
29	chr2:234206000-234215400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr2:234206000-234218600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr2:234206400-234209000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr2:234206400-234209600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr2:234206400-234213600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr2:234206400-234216200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr2:234206400-234218800	Weak transcription	Right Atrium	heart
36	chr2:234206600-234209200	Weak transcription	HepG2	liver
37	chr2:234206600-234209400	Weak transcription	Fetal Stomach	stomach
38	chr2:234206800-234209400	Weak transcription	HSMMtube	muscle
39	chr2:234206800-234210800	Weak transcription	A549	lung
40	chr2:234207800-234210400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
41	chr2:234207800-234216000	Weak transcription	H9 Cell Line	embryonic stem cell

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