Variant report

Variant	rs12705071
Chromosome Location	chr7:99682026-99682027
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10228764	0.91[EUR][1000 genomes]
rs10267212	0.82[CEU][hapmap]
rs10281368	1.00[CEU][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs1060544	0.91[EUR][1000 genomes]
rs1076237	0.81[CEU][hapmap]
rs11771139	0.93[TSI][hapmap]
rs12705070	1.00[CEU][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs13223792	1.00[CEU][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs13232115	0.88[EUR][1000 genomes]
rs1534310	0.94[EUR][1000 genomes]
rs1880949	0.97[TSI][hapmap]
rs2070215	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2293479	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs34031156	0.96[EUR][1000 genomes]
rs35146811	0.97[TSI][hapmap]
rs4134903	0.95[CEU][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs4424195	1.00[CEU][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs4729576	0.92[EUR][1000 genomes]
rs59261051	0.95[EUR][1000 genomes]
rs6465760	0.82[CEU][hapmap]
rs6465761	0.91[EUR][1000 genomes]
rs6465762	0.90[EUR][1000 genomes]
rs6950205	0.95[EUR][1000 genomes]
rs6953441	0.91[EUR][1000 genomes]
rs6974305	0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1829865	chr7:99430678-99755141	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1131 gene(s)	inside rSNPs	diseases
2	esv1830649	chr7:99430678-99755141	Strong transcription Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1131 gene(s)	inside rSNPs	diseases
3	nsv534298	chr7:99478011-99886076	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1132 gene(s)	inside rSNPs	diseases
4	nsv469687	chr7:99572543-99755141	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1115 gene(s)	inside rSNPs	diseases
5	nsv482601	chr7:99572543-99755141	Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1115 gene(s)	inside rSNPs	diseases
6	nsv607931	chr7:99664817-99796146	Bivalent Enhancer Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1097 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs12705071	ZNF498	cis	cerebellum	SCAN
rs12705071	BUD31	cis	parietal	SCAN
rs12705071	ZSCAN21	cis	parietal	SCAN
rs12705071	LRRC17	cis	parietal	SCAN
rs12705071	GATS	cis	parietal	SCAN
rs12705071	GATS	cis	cerebellum	SCAN
rs12705071	ZKSCAN1	cis	cerebellum	SCAN
rs12705071	GAL3ST4	cis	cerebellum	SCAN
rs12705071	SERPINE1	cis	cerebellum	SCAN
rs12705071	GATS	cis	lymphoblastoid	seeQTL
rs12705071	PILRB	cis	parietal	SCAN

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:99679400-99683200	Weak transcription	NHDF-Ad	bronchial
2	chr7:99679400-99684400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr7:99679400-99684400	Weak transcription	NHLF	lung
4	chr7:99679400-99684600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr7:99679400-99686000	Weak transcription	Gastric	stomach
6	chr7:99679400-99686000	Weak transcription	Small Intestine	intestine
7	chr7:99680000-99684600	Weak transcription	A549	lung
8	chr7:99680000-99684800	Weak transcription	Colon Smooth Muscle	Colon
9	chr7:99680200-99685800	Weak transcription	Right Atrium	heart
10	chr7:99680400-99682200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr7:99680400-99683400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr7:99680400-99684400	Weak transcription	Rectal Smooth Muscle	rectum
13	chr7:99680400-99684400	Weak transcription	HMEC	breast
14	chr7:99680400-99684400	Weak transcription	NHEK	skin
15	chr7:99680400-99684600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr7:99680400-99685000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr7:99680400-99685600	Weak transcription	Dnd41	blood
18	chr7:99680600-99683200	Weak transcription	Placenta	Placenta
19	chr7:99680600-99683400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr7:99680600-99684400	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr7:99680600-99684400	Weak transcription	Osteobl	bone
22	chr7:99680600-99684600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr7:99680600-99684600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr7:99680600-99684600	Weak transcription	Hela-S3	cervix
25	chr7:99680600-99685000	Weak transcription	Stomach Smooth Muscle	stomach
26	chr7:99680600-99685600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr7:99680600-99685600	Weak transcription	Brain Hippocampus Middle	brain
28	chr7:99680600-99685600	Weak transcription	Brain Substantia Nigra	brain
29	chr7:99680600-99685600	Weak transcription	Spleen	Spleen
30	chr7:99680600-99686000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr7:99680600-99686000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr7:99680600-99686000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr7:99680600-99686000	Weak transcription	Left Ventricle	heart
34	chr7:99680600-99686000	Weak transcription	Pancreas	Pancrea
35	chr7:99680800-99682800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr7:99680800-99683200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr7:99680800-99683200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr7:99680800-99683800	Weak transcription	Fetal Stomach	stomach
39	chr7:99680800-99684600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr7:99680800-99684600	Weak transcription	NH-A	brain
41	chr7:99680800-99685400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr7:99680800-99685400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
43	chr7:99680800-99685600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr7:99680800-99685600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr7:99680800-99685600	Weak transcription	Primary T helper cells PMA-I stimulated	--
46	chr7:99680800-99685600	Weak transcription	Primary T helper cells fromperipheralblood	blood
47	chr7:99680800-99685600	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr7:99680800-99685600	Weak transcription	Fetal Intestine Large	intestine
49	chr7:99680800-99685600	Weak transcription	Fetal Intestine Small	intestine
50	chr7:99680800-99685600	Weak transcription	Fetal Kidney	kidney

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