Variant report

Variant	rs56172865
Chromosome Location	chr2:160967333-160967334
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	chr2:160750717..160753451-chr2:160965407..160967520,2	MCF-7	breast:
2	chr2:160964387..160968256-chr2:161077211..161080822,5	MCF-7	breast:

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10497213	0.96[ASN][1000 genomes]
rs10929965	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10929966	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12987602	0.96[ASN][1000 genomes]
rs1511218	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs16844715	0.80[EUR][1000 genomes]
rs17216980	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17241792	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17241973	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17341301	0.85[EUR][1000 genomes]
rs17831161	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17831191	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17831251	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17831329	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2124969	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2175416	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2305819	0.81[ASN][1000 genomes]
rs34248629	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3749119	0.84[ASN][1000 genomes]
rs4233681	0.96[ASN][1000 genomes]
rs4292050	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4363984	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4520993	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4520994	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4637057	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4664308	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4665147	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4665148	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56293836	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs56297666	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs58354887	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62175515	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62175517	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62175552	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62175559	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62177860	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62177891	0.82[ASN][1000 genomes]
rs6707388	0.95[ASN][1000 genomes]
rs6707458	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6719686	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6728154	0.83[ASN][1000 genomes]
rs6731260	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6739867	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6744567	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6759836	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7563607	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7593593	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs877200	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs925410	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv459929	chr2:160963603-161079435	Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv583497	chr2:160963603-161079435	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv875346	chr2:160965335-161044155	Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:160953200-160970800	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr2:160954600-160970800	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr2:160954600-160993000	Weak transcription	Duodenum Mucosa	Duodenum
4	chr2:160955800-160968800	Weak transcription	Fetal Muscle Trunk	muscle
5	chr2:160957000-160970200	Weak transcription	Pancreas	Pancrea
6	chr2:160957400-160981200	Weak transcription	Lung	lung
7	chr2:160959200-161004200	Weak transcription	Gastric	stomach
8	chr2:160959400-160985200	Weak transcription	Esophagus	oesophagus
9	chr2:160959400-161032800	Weak transcription	Psoas Muscle	Psoas
10	chr2:160962400-160970800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr2:160962800-160971000	Strong transcription	Placenta Amnion	Placenta Amnion
12	chr2:160963800-160969200	Strong transcription	Skeletal Muscle Male	skeletal muscle
13	chr2:160964200-160993600	Weak transcription	Fetal Muscle Leg	muscle
14	chr2:160964400-160993600	Weak transcription	Fetal Intestine Large	intestine
15	chr2:160964800-160970800	Weak transcription	Stomach Mucosa	stomach
16	chr2:160965000-160968200	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr2:160965200-160968000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr2:160965600-160967600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr2:160965600-160968000	Genic enhancers	NHEK	skin
20	chr2:160965600-160969200	Genic enhancers	HMEC	breast
21	chr2:160965800-160969600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr2:160966000-160968000	Enhancers	A549	lung
23	chr2:160966200-160969000	Strong transcription	Fetal Intestine Small	intestine
24	chr2:160966400-160968600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr2:160966400-160970600	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr2:160966400-160980200	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr2:160966600-160967600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr2:160967000-160967400	Enhancers	H1 Cell Line	embryonic stem cell
29	chr2:160967000-160967400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr2:160967000-160967800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr2:160967000-160968400	Enhancers	GM12878-XiMat	blood
32	chr2:160967000-160969400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr2:160967200-160970400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr2:160967200-160979000	Weak transcription	HSMM	muscle

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