Variant report

Variant	rs11883977
Chromosome Location	chr2:172807590-172807591
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:172807475..172809452-chr2:172960168..172961803,2	MCF-7	breast:
2	chr2:172778216..172780753-chr2:172807408..172809442,2	K562	blood:
3	chr2:172806807..172809345-chr2:172947869..172949809,2	MCF-7	breast:
4	chr2:172807381..172810249-chr2:172812203..172814108,2	K562	blood:
5	chr2:172801698..172803209-chr2:172806967..172809271,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000144355	Chromatin interaction
ENSG00000128708	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10166352	0.91[ASN][1000 genomes]
rs10177679	0.82[ASN][1000 genomes]
rs10188587	0.82[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs10439296	0.93[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs10930498	0.98[ASN][1000 genomes]
rs10930500	0.88[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs10930501	0.82[AFR][1000 genomes]
rs11676484	0.86[AFR][1000 genomes]
rs11677573	0.82[ASN][1000 genomes]
rs11692418	0.87[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs11695887	0.98[ASN][1000 genomes]
rs12467010	0.91[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs12468218	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12478215	0.98[ASN][1000 genomes]
rs13017988	0.91[ASN][1000 genomes]
rs13018515	0.84[ASN][1000 genomes]
rs13399316	0.93[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs1443700	0.90[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs1982288	0.94[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs2028670	0.87[AFR][1000 genomes]
rs2028671	0.90[AFR][1000 genomes]
rs2028672	0.91[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs2028673	0.88[AFR][1000 genomes]
rs2028674	0.88[AFR][1000 genomes]
rs2357207	0.91[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs2357208	0.93[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs28372952	0.84[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs4072279	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4324292	0.93[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs4668419	0.91[ASN][1000 genomes]
rs59853867	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs60706248	0.91[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs6433318	0.93[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs6707142	0.90[AFR][1000 genomes]
rs6714214	0.90[AFR][1000 genomes]
rs6726050	0.94[AFR][1000 genomes]
rs6740705	0.89[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs6741030	0.90[AFR][1000 genomes]
rs6742905	0.82[ASN][1000 genomes]
rs6753551	0.86[AFR][1000 genomes]
rs6757680	0.92[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs6758494	0.86[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs7340516	0.87[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs7371503	0.84[ASN][1000 genomes]
rs7579509	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7580132	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7594478	0.83[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs7597525	0.82[ASN][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	nsv875410	chr2:172693780-172896587	Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv875411	chr2:172693780-172942448	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	esv2830399	chr2:172781830-172952526	Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:172779800-172828400	Weak transcription	Aorta	Aorta
2	chr2:172780000-172812800	Weak transcription	Lung	lung
3	chr2:172780000-172829000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr2:172780200-172822200	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr2:172780200-172840400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr2:172780400-172820600	Weak transcription	Brain Angular Gyrus	brain
7	chr2:172780400-172848800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr2:172780600-172811200	Weak transcription	HSMMtube	muscle
9	chr2:172780600-172811200	Weak transcription	NHEK	skin
10	chr2:172780600-172820600	Weak transcription	Brain Anterior Caudate	brain
11	chr2:172780600-172822200	Weak transcription	Liver	Liver
12	chr2:172780600-172822200	Weak transcription	Fetal Kidney	kidney
13	chr2:172780600-172847400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr2:172780600-172854200	Weak transcription	Small Intestine	intestine
15	chr2:172781000-172811000	Weak transcription	Right Ventricle	heart
16	chr2:172781000-172811200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr2:172781200-172808800	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr2:172781200-172811200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr2:172781400-172822000	Weak transcription	HUVEC	blood vessel
20	chr2:172783600-172851000	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr2:172783800-172811200	Weak transcription	HMEC	breast
22	chr2:172784000-172811400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr2:172784200-172811200	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr2:172784600-172815000	Weak transcription	Left Ventricle	heart
25	chr2:172785000-172811200	Weak transcription	Adipose Nuclei	Adipose
26	chr2:172785400-172822200	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr2:172785400-172822400	Weak transcription	Placenta	Placenta
28	chr2:172785800-172822200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr2:172787000-172811400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr2:172787200-172812800	Weak transcription	Fetal Brain Male	brain
31	chr2:172787400-172810600	Weak transcription	Hela-S3	cervix
32	chr2:172787600-172809600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr2:172787800-172822200	Weak transcription	Brain Hippocampus Middle	brain
34	chr2:172788000-172809600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr2:172788000-172811400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr2:172788000-172811400	Weak transcription	Fetal Intestine Large	intestine
37	chr2:172788000-172811800	Weak transcription	Ovary	ovary
38	chr2:172788000-172812600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr2:172788200-172809600	Weak transcription	Thymus	Thymus
40	chr2:172788400-172810600	Weak transcription	GM12878-XiMat	blood
41	chr2:172788400-172811200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr2:172788400-172812800	Weak transcription	Pancreas	Pancrea
43	chr2:172788600-172810800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr2:172788800-172809600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr2:172788800-172811400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr2:172789000-172808400	Weak transcription	Primary hematopoietic stem cells	blood
47	chr2:172789000-172810600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
48	chr2:172789400-172809600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr2:172789400-172810600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
50	chr2:172790000-172808200	Weak transcription	Primary B cells from cord blood	blood

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