Variant report

Variant	rs10200243
Chromosome Location	chr2:182651182-182651183
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:182647541..182657734-chr2:182753295..182760748,23	MCF-7	breast:
2	chr2:182642988..182645048-chr2:182649419..182652084,2	MCF-7	breast:
3	chr2:182649909..182651915-chr2:182653150..182656385,3	MCF-7	breast:
4	chr2:182650516..182651413-chr2:182740843..182741530,2	Hela-S3	cervix:
5	chr2:182646086..182659083-chr2:182754079..182762654,36	MCF-7	breast:
6	chr2:182607060..182610718-chr2:182648609..182651704,3	MCF-7	breast:
7	chr2:182642047..182644183-chr2:182648360..182651289,2	K562	blood:

Variant related genes	Relation type
ENSG00000260742	Chromatin interaction
ENSG00000138434	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10165226	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10165936	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10166812	0.83[YRI][hapmap];0.82[AFR][1000 genomes]
rs10173114	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10176061	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10176613	1.00[CEU][hapmap]
rs10176757	1.00[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap];0.82[EUR][1000 genomes]
rs10179363	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10179547	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10182213	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10199645	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10201303	1.00[CEU][hapmap]
rs10210215	1.00[CEU][hapmap]
rs10221891	1.00[CEU][hapmap];0.88[TSI][hapmap]
rs1106013	0.92[ASN][1000 genomes]
rs13404156	1.00[CEU][hapmap]
rs13425734	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1528024	1.00[CEU][hapmap]
rs1528025	1.00[CEU][hapmap]
rs1528027	1.00[CEU][hapmap]
rs16867498	1.00[CEU][hapmap]
rs16867500	0.82[JPT][hapmap]
rs16867509	1.00[CEU][hapmap]
rs1881158	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1881159	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2059702	1.00[CEU][hapmap]
rs2288330	1.00[CEU][hapmap]
rs2303554	1.00[CEU][hapmap]
rs2368224	1.00[CEU][hapmap]
rs3731693	1.00[CEU][hapmap]
rs3815877	1.00[CEU][hapmap]
rs3815878	1.00[CEU][hapmap]
rs6433943	1.00[CEU][hapmap]
rs6707164	1.00[CEU][hapmap]
rs6720109	1.00[CEU][hapmap]
rs6720702	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6730859	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6735322	1.00[CEU][hapmap]
rs6736766	1.00[CEU][hapmap]
rs6748354	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6751685	1.00[CEU][hapmap]
rs6754192	1.00[CEU][hapmap]
rs6755017	1.00[CEU][hapmap]
rs7557969	1.00[CEU][hapmap]
rs7562680	1.00[CEU][hapmap]
rs7580410	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7603721	1.00[CEU][hapmap]
rs7608942	1.00[CEU][hapmap]
rs937297	0.92[ASN][1000 genomes]
rs950165	0.92[ASN][1000 genomes]
rs9807949	1.00[CEU][hapmap]
rs9808112	1.00[CEU][hapmap]
rs9808113	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[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	nsv1005870	chr2:181968637-182921439	Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv536063	chr2:181968637-182921439	Enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv1001558	chr2:182590009-182732738	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10200243	LOC647288///LOC730587	trans	lymphoblastoid	RTeQTL

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:182642200-182657200	Enhancers	Hela-S3	cervix
2	chr2:182645200-182651800	Weak transcription	Thymus	Thymus
3	chr2:182646000-182651200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr2:182646000-182651800	Weak transcription	Fetal Thymus	thymus
5	chr2:182646200-182651200	Weak transcription	Primary hematopoietic stem cells	blood
6	chr2:182646200-182651200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr2:182646400-182651600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr2:182646400-182651600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr2:182646600-182651200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr2:182646600-182651200	Weak transcription	Pancreas	Pancrea
11	chr2:182646600-182653400	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr2:182646600-182654800	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr2:182647200-182652600	Enhancers	HepG2	liver
14	chr2:182647200-182652800	Enhancers	Stomach Mucosa	stomach
15	chr2:182647400-182653000	Enhancers	Fetal Intestine Small	intestine
16	chr2:182648000-182657200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr2:182648200-182651200	Weak transcription	Placenta	Placenta
18	chr2:182648200-182651800	Weak transcription	Dnd41	blood
19	chr2:182648600-182651200	Enhancers	Placenta Amnion	Placenta Amnion
20	chr2:182648600-182651400	Enhancers	Osteobl	bone
21	chr2:182648600-182657200	Enhancers	HMEC	breast
22	chr2:182648800-182654600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr2:182648800-182657000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr2:182649000-182651400	Enhancers	HSMM	muscle
25	chr2:182649200-182651400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr2:182649200-182651400	Enhancers	Rectal Mucosa Donor 31	rectum
27	chr2:182649200-182651400	Enhancers	NHDF-Ad	bronchial
28	chr2:182649200-182656200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr2:182649400-182651600	Enhancers	NHLF	lung
30	chr2:182649600-182654800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr2:182649600-182657200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr2:182650000-182651400	Enhancers	A549	lung
33	chr2:182650000-182653600	Weak transcription	Duodenum Mucosa	Duodenum
34	chr2:182650000-182655400	Enhancers	NHEK	skin
35	chr2:182650200-182657000	Enhancers	Fetal Intestine Large	intestine
36	chr2:182650400-182652400	Enhancers	Fetal Kidney	kidney
37	chr2:182650600-182651200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr2:182650600-182652000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr2:182650800-182651200	Enhancers	Muscle Satellite Cultured Cells	--
40	chr2:182650800-182652200	Weak transcription	HUVEC	blood vessel
41	chr2:182650800-182654800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr2:182651000-182651800	Enhancers	Small Intestine	intestine
43	chr2:182651000-182652000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr2:182651000-182653600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr2:182651000-182653600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr2:182651000-182653600	Weak transcription	NH-A	brain
47	chr2:182651000-182655600	Weak transcription	HSMMtube	muscle
48	chr2:182651000-182655800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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