Variant report

Variant	rs2345644
Chromosome Location	chr2:153056973-153056974
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	chr2:153056708..153058383-chr2:153191283..153193021,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000157827	Chromatin interaction

Extended variants
information (count: 98 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10182046	0.82[EUR][1000 genomes]
rs10194916	0.90[CEU][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs10200231	0.82[EUR][1000 genomes]
rs10930984	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10930988	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11683326	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11684002	0.94[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11684622	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11695538	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12999722	0.80[EUR][1000 genomes]
rs13023172	0.86[EUR][1000 genomes]
rs13027360	0.82[EUR][1000 genomes]
rs17326195	0.84[CEU][hapmap];0.85[EUR][1000 genomes]
rs17398246	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17398253	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17398399	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1987371	0.83[EUR][1000 genomes]
rs2004544	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2345646	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2345811	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2345816	0.86[EUR][1000 genomes]
rs2345886	0.86[EUR][1000 genomes]
rs2345887	0.86[EUR][1000 genomes]
rs2345888	0.85[EUR][1000 genomes]
rs2345889	0.86[EUR][1000 genomes]
rs2345890	0.86[EUR][1000 genomes]
rs2345891	0.86[EUR][1000 genomes]
rs2345892	0.86[EUR][1000 genomes]
rs2345893	0.80[EUR][1000 genomes]
rs2345894	0.90[CEU][hapmap];1.00[JPT][hapmap]
rs2345897	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2345900	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2346203	1.00[JPT][hapmap]
rs2881237	0.84[EUR][1000 genomes]
rs2881238	0.86[EUR][1000 genomes]
rs2881242	0.82[EUR][1000 genomes]
rs35451141	0.81[EUR][1000 genomes]
rs4233656	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4233657	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4254462	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4284784	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4293527	0.86[EUR][1000 genomes]
rs4316898	0.86[EUR][1000 genomes]
rs4664090	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs4664092	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4664548	0.81[EUR][1000 genomes]
rs4664549	0.86[EUR][1000 genomes]
rs4664551	0.86[EUR][1000 genomes]
rs4664552	0.85[EUR][1000 genomes]
rs4664556	0.80[EUR][1000 genomes]
rs4664558	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs56853020	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60098187	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60847003	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6433898	0.89[EUR][1000 genomes]
rs6433929	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6433933	0.85[EUR][1000 genomes]
rs6433935	0.86[EUR][1000 genomes]
rs6433940	0.85[EUR][1000 genomes]
rs66529470	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66530032	0.85[EUR][1000 genomes]
rs66673544	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs66733611	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs66782719	0.85[EUR][1000 genomes]
rs6712158	0.86[EUR][1000 genomes]
rs67135983	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs67157738	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6726065	0.85[EUR][1000 genomes]
rs6729673	0.86[EUR][1000 genomes]
rs6745311	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6746538	1.00[JPT][hapmap]
rs6747394	0.85[EUR][1000 genomes]
rs6750417	0.85[EUR][1000 genomes]
rs6750670	0.85[EUR][1000 genomes]
rs67874818	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68008008	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs68036808	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72857737	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72859833	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72859836	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72864740	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72864741	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72864754	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72864765	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73002815	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7570050	0.86[EUR][1000 genomes]
rs7579128	0.86[EUR][1000 genomes]
rs7586518	0.85[EUR][1000 genomes]
rs7597103	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7600346	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005746	chr2:152361972-153059840	Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv535984	chr2:152361972-153059840	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv875287	chr2:152714680-153110573	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv875288	chr2:152716628-153183646	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv875289	chr2:152720030-153183646	Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
6	nsv1004308	chr2:152980087-153154534	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
7	nsv535985	chr2:152980087-153154534	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
8	esv3693434	chr2:152998467-153208713	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:153053400-153057000	Weak transcription	Placenta	Placenta
2	chr2:153055400-153057400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr2:153055600-153057000	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr2:153055600-153057000	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr2:153055600-153057000	Weak transcription	HepG2	liver
6	chr2:153056200-153057000	Enhancers	NHEK	skin
7	chr2:153056200-153057200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr2:153056200-153057800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr2:153056400-153057000	Enhancers	NHDF-Ad	bronchial
10	chr2:153056400-153057200	Enhancers	HUVEC	blood vessel
11	chr2:153056400-153057400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr2:153056400-153057400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr2:153056400-153057400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr2:153056400-153057800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr2:153056400-153058200	Enhancers	Hela-S3	cervix
16	chr2:153056400-153058400	Enhancers	HMEC	breast
17	chr2:153056600-153057000	Enhancers	Muscle Satellite Cultured Cells	--
18	chr2:153056600-153057200	Enhancers	Osteobl	bone
19	chr2:153056600-153057400	Enhancers	NHLF	lung
20	chr2:153056600-153057600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr2:153056600-153057600	Enhancers	Brain Substantia Nigra	brain
22	chr2:153056600-153057600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
23	chr2:153056600-153057600	Enhancers	HSMM	muscle
24	chr2:153056600-153058200	Enhancers	Brain Germinal Matrix	brain
25	chr2:153056800-153057000	Flanking Active TSS	A549	lung
26	chr2:153056800-153057000	Enhancers	K562	blood
27	chr2:153056800-153057000	Enhancers	NH-A	brain
28	chr2:153056800-153057600	Enhancers	ES-I3 Cell Line	embryonic stem cell
29	chr2:153056800-153057600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr2:153056800-153057600	Enhancers	Brain Hippocampus Middle	brain
31	chr2:153056800-153057800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr2:153056800-153057800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr2:153056800-153057800	Enhancers	Stomach Mucosa	stomach

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