Variant report

Variant	rs12991571
Chromosome Location	chr2:20367289-20367290
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:20362106..20364188-chr2:20366369..20369040,2	MCF-7	breast:
2	chr2:20366533..20369508-chr2:20380029..20382114,2	MCF-7	breast:
3	chr2:20364027..20368295-chr2:20377113..20381748,5	MCF-7	breast:
4	chr2:20364604..20368497-chr2:20376297..20379611,4	MCF-7	breast:
5	chr2:20366147..20368368-chr2:20415586..20417297,2	MCF-7	breast:
6	chr2:20365445..20367731-chr2:20374746..20377053,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000200763	Chromatin interaction
ENSG00000266059	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs12987877	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs16987398	0.86[MEX][hapmap];0.83[AMR][1000 genomes]
rs16987405	0.85[AMR][1000 genomes]
rs16987429	0.95[CHB][hapmap];0.91[JPT][hapmap];0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4392207	0.84[EUR][1000 genomes]
rs4666296	0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4666363	0.85[AMR][1000 genomes]
rs4666367	0.86[AMR][1000 genomes]
rs4666371	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4666373	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs56736615	0.85[AMR][1000 genomes]
rs71435550	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7583442	0.95[CHB][hapmap];0.83[CHD][hapmap];0.91[JPT][hapmap];0.86[MEX][hapmap];0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009521	chr2:20310479-20388959	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv1012841	chr2:20328894-20415168	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv1004083	chr2:20336237-20388138	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv1000323	chr2:20336237-20419923	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv1004947	chr2:20342264-20388138	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv1005923	chr2:20344028-20369781	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
7	nsv997958	chr2:20349343-20386339	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv1005524	chr2:20349343-20388138	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
9	nsv999131	chr2:20350751-20377607	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	nsv998067	chr2:20350751-20386339	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
11	nsv1001531	chr2:20350751-20388138	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
12	nsv1007926	chr2:20350751-20393557	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
13	esv3451715	chr2:20363271-20367769	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12991571	LPAR6	trans	lymphoblastoid	seeQTL

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20362400-20371400	Weak transcription	Right Atrium	heart
2	chr2:20363800-20374000	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr2:20364000-20367800	Enhancers	A549	lung
4	chr2:20364000-20368000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr2:20364200-20368000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr2:20364200-20369200	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr2:20364400-20367400	Enhancers	GM12878-XiMat	blood
8	chr2:20364400-20367400	Enhancers	NHDF-Ad	bronchial
9	chr2:20364400-20372000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr2:20364600-20367600	Enhancers	HMEC	breast
11	chr2:20364800-20372200	Enhancers	NHEK	skin
12	chr2:20365000-20368400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr2:20365000-20368600	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr2:20365200-20367400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr2:20365200-20367600	Enhancers	NH-A	brain
16	chr2:20365600-20367400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr2:20365600-20367400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr2:20365600-20367400	Enhancers	Osteobl	bone
19	chr2:20365600-20367800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr2:20365800-20367400	Enhancers	Muscle Satellite Cultured Cells	--
21	chr2:20365800-20367400	Enhancers	HSMM	muscle
22	chr2:20365800-20367600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
23	chr2:20365800-20367600	Enhancers	Pancreas	Pancrea
24	chr2:20365800-20367800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr2:20365800-20368400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
26	chr2:20365800-20369800	Weak transcription	Lung	lung
27	chr2:20366000-20367400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr2:20366000-20367400	Enhancers	HSMMtube	muscle
29	chr2:20366000-20367600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr2:20366000-20367600	Enhancers	Esophagus	oesophagus
31	chr2:20366000-20369600	Enhancers	Rectal Mucosa Donor 31	rectum
32	chr2:20366000-20370400	Weak transcription	Fetal Kidney	kidney
33	chr2:20366000-20370800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr2:20366000-20371200	Weak transcription	Fetal Lung	lung
35	chr2:20366200-20369000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr2:20366400-20367400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr2:20366400-20367800	Bivalent Enhancer	HepG2	liver
38	chr2:20366400-20369200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr2:20366400-20372000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr2:20366600-20367800	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr2:20366600-20369200	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr2:20366600-20369800	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr2:20366600-20371600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr2:20366800-20367600	Enhancers	Fetal Heart	heart
45	chr2:20366800-20369400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr2:20366800-20369800	Weak transcription	Fetal Intestine Small	intestine
47	chr2:20366800-20369800	Weak transcription	HUVEC	blood vessel
48	chr2:20366800-20372600	Enhancers	Placenta	Placenta
49	chr2:20367000-20367600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr2:20367000-20369200	Enhancers	Colonic Mucosa	Colon

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