Variant report

Variant	rs13031549
Chromosome Location	chr2:190030816-190030817
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:190016341..190018052-chr2:190028651..190030939,2	MCF-7	breast:
2	chr2:190029422..190031666-chr2:190149954..190151681,2	MCF-7	breast:
3	chr2:190030141..190032156-chr2:190304777..190307765,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115368	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10931400	0.85[EUR][1000 genomes]
rs10931404	0.89[ASN][1000 genomes]
rs11681286	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11691604	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12104769	0.85[EUR][1000 genomes]
rs12105389	0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12611950	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12615823	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12618438	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12621035	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12621806	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12621939	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12991770	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12993719	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12995956	0.85[EUR][1000 genomes]
rs12999122	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12999996	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13005652	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13005821	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13011374	0.85[ASN][1000 genomes]
rs13012327	0.90[ASN][1000 genomes]
rs13012649	0.84[EUR][1000 genomes]
rs13015283	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13016231	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13017413	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13019076	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13021508	0.87[ASN][1000 genomes]
rs13022633	0.86[ASN][1000 genomes]
rs13028967	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13029705	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13031211	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13033421	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1356162	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1356163	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1356164	0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1356165	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1356167	0.93[CEU][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1356168	0.92[CEU][hapmap];0.80[JPT][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1399991	0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1399992	0.90[ASN][1000 genomes]
rs1515874	0.90[ASN][1000 genomes]
rs1515876	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1878085	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1949484	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1965422	0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2138374	0.85[CEU][hapmap];0.81[JPT][hapmap];0.83[EUR][1000 genomes]
rs2222256	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2351627	0.85[EUR][1000 genomes]
rs35475196	0.89[ASN][1000 genomes]
rs35772309	0.89[ASN][1000 genomes]
rs3914778	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4233801	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4428040	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4667264	0.93[CEU][hapmap];0.80[JPT][hapmap];0.85[EUR][1000 genomes]
rs4667265	0.93[CEU][hapmap];0.81[JPT][hapmap];0.85[EUR][1000 genomes]
rs4667272	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4667274	0.84[ASN][1000 genomes]
rs4998559	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60124911	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6434339	0.82[CEU][hapmap];0.81[CHB][hapmap];0.91[JPT][hapmap]
rs6708419	0.93[CEU][hapmap];0.81[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6714088	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6719104	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6737071	0.86[EUR][1000 genomes]
rs7419888	0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7561002	0.93[CEU][hapmap];0.81[EUR][1000 genomes]
rs7564611	0.87[ASN][1000 genomes]
rs7576165	0.85[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs7587147	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7587956	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7607133	0.81[ASN][1000 genomes]
rs7609495	0.91[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	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	nsv875613	chr2:189999011-190324685	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:190019600-190040000	Weak transcription	Fetal Intestine Small	intestine
2	chr2:190021000-190031400	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr2:190026600-190032000	Enhancers	HUES48 Cell Line	embryonic stem cell
4	chr2:190027600-190032000	Enhancers	Fetal Lung	lung
5	chr2:190027800-190031400	Enhancers	NH-A	brain
6	chr2:190028000-190032800	Enhancers	NHLF	lung
7	chr2:190028400-190033800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr2:190028800-190034200	Enhancers	Liver	Liver
9	chr2:190029000-190031200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr2:190029000-190031400	Weak transcription	Stomach Smooth Muscle	stomach
11	chr2:190029000-190033600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr2:190029000-190037200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr2:190029200-190031200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr2:190029200-190033600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr2:190029400-190040800	Weak transcription	Fetal Kidney	kidney
16	chr2:190029400-190042200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr2:190029600-190031000	Weak transcription	HSMMtube	muscle
18	chr2:190029600-190032600	Enhancers	Fetal Muscle Leg	muscle
19	chr2:190029600-190043400	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr2:190029800-190031400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr2:190029800-190031400	Weak transcription	Rectal Smooth Muscle	rectum
22	chr2:190029800-190031400	Weak transcription	HMEC	breast
23	chr2:190029800-190033600	Enhancers	A549	lung
24	chr2:190029800-190036800	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr2:190029800-190043200	Weak transcription	Psoas Muscle	Psoas
26	chr2:190030000-190032000	Genic enhancers	HSMM	muscle
27	chr2:190030000-190036600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr2:190030000-190041200	Weak transcription	HUVEC	blood vessel
29	chr2:190030200-190031000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr2:190030200-190031000	Enhancers	iPS-15b Cell Line	embryonic stem cell
31	chr2:190030200-190031400	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr2:190030200-190031400	Genic enhancers	Osteobl	bone
33	chr2:190030200-190034400	Weak transcription	Fetal Muscle Trunk	muscle
34	chr2:190030200-190041200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr2:190030400-190031400	Weak transcription	Ovary	ovary
36	chr2:190030400-190036600	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr2:190030400-190043400	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr2:190030600-190031400	Weak transcription	Adipose Nuclei	Adipose
39	chr2:190030600-190032200	Enhancers	Colon Smooth Muscle	Colon
40	chr2:190030600-190033600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr2:190030600-190033600	Weak transcription	Fetal Stomach	stomach
42	chr2:190030600-190033800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr2:190030600-190033800	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr2:190030800-190031000	Enhancers	H1 Cell Line	embryonic stem cell
45	chr2:190030800-190031000	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr2:190030800-190031000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr2:190030800-190031400	Genic enhancers	Muscle Satellite Cultured Cells	--
48	chr2:190030800-190031600	Enhancers	Aorta	Aorta
49	chr2:190030800-190032000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr2:190030800-190032000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin

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