Variant report

Variant	rs4998559
Chromosome Location	chr2:190034971-190034972
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:190033187..190035934-chr2:190088474..190090590,2	MCF-7	breast:
2	chr2:190027832..190030639-chr2:190032693..190035632,2	MCF-7	breast:

Extended variants
information (count: 92 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs10931400	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10931404	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11681286	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11691604	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12104769	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12105389	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12611950	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12615823	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12618438	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12621035	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12621806	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12621939	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12991770	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12993719	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12995956	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12999122	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12999996	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13004722	0.86[EUR][1000 genomes]
rs13005652	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13005714	0.81[YRI][hapmap]
rs13005821	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13011374	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13011485	0.87[EUR][1000 genomes]
rs13012327	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13012649	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13015283	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13016231	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13017413	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13019076	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13020999	0.84[YRI][hapmap]
rs13021508	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13022633	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13028967	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13029705	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13030984	0.82[YRI][hapmap]
rs13031211	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13031549	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]
rs13033421	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1356162	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1356163	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1356164	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1356165	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[YRI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1356167	1.00[CEU][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1356168	1.00[CEU][hapmap];0.80[JPT][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1399991	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1399992	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1464135	0.84[YRI][hapmap]
rs1515864	0.84[YRI][hapmap]
rs1515874	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1515876	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1568334	0.87[EUR][1000 genomes]
rs1878085	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1949327	0.82[YRI][hapmap]
rs1949484	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1965422	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]
rs2138373	0.80[YRI][hapmap]
rs2138374	0.92[CEU][hapmap];0.81[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2222256	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2351627	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2351636	0.86[EUR][1000 genomes]
rs35475196	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35772309	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3914778	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4233801	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4417749	0.82[YRI][hapmap]
rs4428040	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4667264	1.00[CEU][hapmap];0.80[JPT][hapmap];0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4667265	1.00[CEU][hapmap];0.81[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4667272	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4667274	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4667276	0.87[EUR][1000 genomes]
rs4667277	0.87[EUR][1000 genomes]
rs60124911	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62182416	0.95[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs6434324	0.81[YRI][hapmap]
rs6434339	0.89[CEU][hapmap];0.81[CHB][hapmap];0.91[JPT][hapmap];0.86[EUR][1000 genomes]
rs6708419	1.00[CEU][hapmap];0.81[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6714088	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6719104	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6737071	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6749559	0.84[YRI][hapmap]
rs7419888	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7560973	0.84[YRI][hapmap]
rs7561002	1.00[CEU][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs7564611	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7576165	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7587147	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7587956	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7607133	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7609495	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[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	chr2:190019600-190040000	Weak transcription	Fetal Intestine Small	intestine
2	chr2:190029000-190037200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr2:190029400-190040800	Weak transcription	Fetal Kidney	kidney
4	chr2:190029400-190042200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr2:190029600-190043400	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr2:190029800-190036800	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr2:190029800-190043200	Weak transcription	Psoas Muscle	Psoas
8	chr2:190030000-190036600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr2:190030000-190041200	Weak transcription	HUVEC	blood vessel
10	chr2:190030200-190041200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr2:190030400-190036600	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr2:190030400-190043400	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr2:190031600-190038800	Weak transcription	Aorta	Aorta
14	chr2:190031800-190035200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr2:190032000-190035000	Weak transcription	NH-A	brain
16	chr2:190032000-190036000	Weak transcription	Fetal Lung	lung
17	chr2:190032000-190036600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr2:190032000-190036600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr2:190032800-190036800	Weak transcription	NHLF	lung
20	chr2:190032800-190037200	Enhancers	Adipose Nuclei	Adipose
21	chr2:190033600-190035000	Enhancers	Osteobl	bone
22	chr2:190034000-190035000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr2:190034000-190035800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr2:190034000-190036600	Weak transcription	Fetal Stomach	stomach
25	chr2:190034000-190040800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr2:190034000-190043400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr2:190034200-190035000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr2:190034200-190035000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr2:190034200-190035000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr2:190034200-190035000	Weak transcription	Rectal Smooth Muscle	rectum
31	chr2:190034200-190035000	Weak transcription	A549	lung
32	chr2:190034200-190035000	Weak transcription	HSMM	muscle
33	chr2:190034200-190035800	Weak transcription	Right Atrium	heart
34	chr2:190034200-190035800	Weak transcription	Small Intestine	intestine
35	chr2:190034200-190036200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr2:190034200-190037600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr2:190034200-190041400	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr2:190034400-190035600	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr2:190034600-190035400	Enhancers	Stomach Smooth Muscle	stomach
40	chr2:190034800-190035200	Enhancers	NHDF-Ad	bronchial
41	chr2:190034800-190035600	Enhancers	Duodenum Smooth Muscle	Duodenum
42	chr2:190034800-190035800	Weak transcription	Ovary	ovary
43	chr2:190034800-190036600	Weak transcription	Fetal Muscle Leg	muscle
44	chr2:190034800-190036600	Enhancers	HSMMtube	muscle
45	chr2:190034800-190037000	Enhancers	Colon Smooth Muscle	Colon
46	chr2:190034800-190040400	Weak transcription	Fetal Muscle Trunk	muscle

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