Variant report

Variant	rs10497671
Chromosome Location	chr2:187374603-187374604
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:187374448..187380167-chr2:187454386..187459436,9	MCF-7	breast:

Variant related genes	Relation type
ENSG00000138448	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10169008	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10169206	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10177153	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10190003	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];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10196955	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10198525	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10200749	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10205170	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10208643	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10931240	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11675633	0.89[ASN][1000 genomes]
rs11688988	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11690758	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11692347	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11888880	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11888881	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11901465	0.89[ASN][1000 genomes]
rs11903027	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12328822	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13392819	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs13397188	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13398352	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13401304	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13428033	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1448848	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1448849	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap]
rs1448855	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1448857	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16827968	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1868383	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2084488	0.89[ASN][1000 genomes]
rs2084489	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2084490	0.84[ASN][1000 genomes]
rs2197139	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2370688	0.89[ASN][1000 genomes]
rs2887826	0.89[ASN][1000 genomes]
rs34234405	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35642346	0.89[ASN][1000 genomes]
rs56137171	0.89[ASN][1000 genomes]
rs61434493	0.89[ASN][1000 genomes]
rs6434174	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6709401	1.00[CHB][hapmap]
rs6710436	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6715493	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6717505	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6717525	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs6721789	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6728382	0.89[ASN][1000 genomes]
rs6728400	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6731567	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs6744717	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.89[ASN][1000 genomes]
rs72895449	0.89[ASN][1000 genomes]
rs7579259	0.89[ASN][1000 genomes]
rs7582412	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7584137	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7585905	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7597954	0.84[AFR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7606920	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9288129	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9917285	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757844	chr2:187332780-187580547	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	esv2759107	chr2:187332780-187580547	Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv459988	chr2:187364878-187440683	Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	nsv584031	chr2:187364878-187440683	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10497671	PNPLA7	trans	brain	seeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:187357000-187379000	Strong transcription	Fetal Thymus	thymus
2	chr2:187357400-187383000	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr2:187357600-187382600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr2:187357600-187386200	Strong transcription	Dnd41	blood
5	chr2:187358200-187379000	Strong transcription	Primary B cells from peripheral blood	blood
6	chr2:187358600-187379000	Strong transcription	HUES64 Cell Line	embryonic stem cell
7	chr2:187358600-187385800	Weak transcription	Esophagus	oesophagus
8	chr2:187358800-187377200	Strong transcription	HepG2	liver
9	chr2:187359000-187376000	Strong transcription	GM12878-XiMat	blood
10	chr2:187359600-187386400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr2:187359800-187374800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr2:187359800-187374800	Strong transcription	Rectal Mucosa Donor 31	rectum
13	chr2:187359800-187375000	Strong transcription	Primary neutrophils fromperipheralblood	blood
14	chr2:187359800-187379000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr2:187359800-187379200	Strong transcription	HUES6 Cell Line	embryonic stem cell
16	chr2:187359800-187379400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr2:187359800-187379800	Strong transcription	HSMM	muscle
18	chr2:187359800-187380400	Strong transcription	HUES48 Cell Line	embryonic stem cell
19	chr2:187359800-187381400	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr2:187359800-187387200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr2:187360000-187376800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr2:187360000-187378600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
23	chr2:187360000-187378800	Strong transcription	Liver	Liver
24	chr2:187360000-187379200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
25	chr2:187360000-187386800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr2:187360200-187374800	Strong transcription	Muscle Satellite Cultured Cells	--
27	chr2:187360200-187374800	Strong transcription	Fetal Intestine Large	intestine
28	chr2:187360200-187375400	Strong transcription	Primary B cells from cord blood	blood
29	chr2:187360200-187376800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr2:187360200-187377000	Strong transcription	Rectal Mucosa Donor 29	rectum
31	chr2:187360200-187378600	Strong transcription	Primary T helper cells PMA-I stimulated	--
32	chr2:187360200-187379000	Strong transcription	Primary T cells fromperipheralblood	blood
33	chr2:187360200-187379200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
34	chr2:187360400-187374800	Strong transcription	Duodenum Mucosa	Duodenum
35	chr2:187360800-187374800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr2:187360800-187379400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr2:187361200-187385600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr2:187361400-187376800	Strong transcription	Osteobl	bone
39	chr2:187361400-187389200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr2:187361800-187377800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr2:187362200-187378400	Strong transcription	K562	blood
42	chr2:187362400-187375800	Strong transcription	H1 Cell Line	embryonic stem cell
43	chr2:187363000-187375200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
44	chr2:187363000-187385600	Weak transcription	Aorta	Aorta
45	chr2:187363000-187387800	Weak transcription	Pancreas	Pancrea
46	chr2:187363000-187408800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr2:187363200-187397600	Weak transcription	Small Intestine	intestine
48	chr2:187363600-187378600	Strong transcription	Primary T helper cells fromperipheralblood	blood
49	chr2:187364000-187374800	Strong transcription	NHDF-Ad	bronchial
50	chr2:187364000-187375000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood

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