Variant report

Variant	rs1965422
Chromosome Location	chr2:190040435-190040436
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:190039205..190041419-chr2:190045253..190047798,2	MCF-7	breast:

Extended variants
information (count: 91 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs10931400	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10931404	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11681286	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11691604	0.84[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12104769	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12105389	0.96[CEU][hapmap];0.94[CHB][hapmap];0.92[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12611950	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12615823	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12618438	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12621035	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12621806	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12621939	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12991770	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12993719	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12995956	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12999122	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12999996	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13004722	0.83[EUR][1000 genomes]
rs13005652	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13005714	0.81[YRI][hapmap]
rs13005821	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13011374	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13011485	0.84[EUR][1000 genomes]
rs13012327	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13012649	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13015283	0.88[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13016231	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13017413	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13019076	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13020999	0.83[YRI][hapmap]
rs13021508	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13022633	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13028967	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13029705	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13030984	0.82[JPT][hapmap];0.82[YRI][hapmap]
rs13031211	0.96[CEU][hapmap];0.94[CHB][hapmap];0.82[JPT][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13031549	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]
rs13033421	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1356162	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1356163	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1356164	0.96[CEU][hapmap];0.94[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1356165	0.96[CEU][hapmap];0.94[CHB][hapmap];0.92[JPT][hapmap];0.88[YRI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1356167	0.96[CEU][hapmap];0.84[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1356168	0.96[CEU][hapmap];0.91[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1399991	0.96[CEU][hapmap];0.94[CHB][hapmap];0.92[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1399992	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1464135	0.83[YRI][hapmap]
rs1515864	0.83[YRI][hapmap]
rs1515874	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1515876	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1568334	0.84[EUR][1000 genomes]
rs1878085	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1949327	0.82[JPT][hapmap];0.82[YRI][hapmap]
rs1949484	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2138373	0.83[YRI][hapmap]
rs2138374	0.89[CEU][hapmap];0.92[JPT][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2222256	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2351627	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2351636	0.83[EUR][1000 genomes]
rs35475196	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35772309	0.90[ASN][1000 genomes]
rs3914778	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4233801	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4417749	0.82[JPT][hapmap];0.82[YRI][hapmap]
rs4428040	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4667264	0.96[CEU][hapmap];0.91[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4667265	0.96[CEU][hapmap];0.92[JPT][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4667272	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4667274	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4667276	0.84[EUR][1000 genomes]
rs4667277	0.84[EUR][1000 genomes]
rs4998559	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60124911	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62182416	0.83[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs6434339	0.85[CEU][hapmap];0.86[JPT][hapmap];0.83[EUR][1000 genomes]
rs6708419	0.96[CEU][hapmap];0.92[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6714088	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6719104	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6737071	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6749559	0.83[YRI][hapmap]
rs7419888	0.96[CEU][hapmap];0.94[CHB][hapmap];0.92[JPT][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7560973	0.83[YRI][hapmap]
rs7561002	0.96[CEU][hapmap];0.84[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs7564611	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7576165	0.88[CEU][hapmap];0.94[CHB][hapmap];0.84[JPT][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7587147	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7587956	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7607133	0.87[EUR][1000 genomes]
rs7609495	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[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:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:190029400-190040800	Weak transcription	Fetal Kidney	kidney
2	chr2:190029400-190042200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr2:190029600-190043400	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr2:190029800-190043200	Weak transcription	Psoas Muscle	Psoas
5	chr2:190030000-190041200	Weak transcription	HUVEC	blood vessel
6	chr2:190030200-190041200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr2:190030400-190043400	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr2:190034000-190040800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr2:190034000-190043400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr2:190034200-190041400	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr2:190036200-190040600	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr2:190037000-190040800	Weak transcription	Right Atrium	heart
13	chr2:190037000-190041000	Weak transcription	Ovary	ovary
14	chr2:190037200-190040600	Weak transcription	Fetal Lung	lung
15	chr2:190037400-190040800	Weak transcription	Fetal Heart	heart
16	chr2:190037400-190040800	Weak transcription	Fetal Stomach	stomach
17	chr2:190037400-190041200	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr2:190037400-190041400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr2:190037400-190042600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr2:190037400-190042600	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr2:190038600-190040600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr2:190038800-190040600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr2:190038800-190040600	Genic enhancers	A549	lung
24	chr2:190038800-190040800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr2:190039200-190040800	Weak transcription	Aorta	Aorta
26	chr2:190039200-190040800	Weak transcription	NHLF	lung
27	chr2:190039600-190040600	Genic enhancers	Muscle Satellite Cultured Cells	--
28	chr2:190039800-190040600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr2:190039800-190040800	Weak transcription	NH-A	brain
30	chr2:190039800-190044800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr2:190040000-190040600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr2:190040000-190040600	ZNF genes & repeats	Fetal Intestine Small	intestine
33	chr2:190040000-190040600	Weak transcription	NHDF-Ad	bronchial
34	chr2:190040000-190040800	Weak transcription	HSMMtube	muscle
35	chr2:190040200-190040600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr2:190040200-190040800	Weak transcription	Osteobl	bone
37	chr2:190040200-190044800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr2:190040400-190040600	Enhancers	Fetal Muscle Trunk	muscle
39	chr2:190040400-190040600	Weak transcription	Fetal Muscle Leg	muscle
40	chr2:190040400-190040600	Enhancers	Stomach Smooth Muscle	stomach
41	chr2:190040400-190040800	Active TSS	HSMM	muscle
42	chr2:190040400-190041000	Enhancers	Colon Smooth Muscle	Colon
43	chr2:190040400-190041200	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr2:190040400-190041400	Flanking Active TSS	Adipose Nuclei	Adipose
45	chr2:190040400-190045000	Active TSS	Rectal Smooth Muscle	rectum
46	chr2:190040400-190045200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin

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