Variant report

Variant	rs7807641
Chromosome Location	chr7:99756503-99756504
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10231604	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11764584	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11771167	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11771331	0.82[YRI][hapmap]
rs12705070	0.89[YRI][hapmap]
rs12878	0.82[ASN][1000 genomes]
rs1527423	0.89[CEU][hapmap]
rs1918352	0.83[EUR][1000 genomes]
rs1918353	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs2272337	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2405440	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34130487	0.82[AFR][1000 genomes]
rs35042434	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3736590	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3736591	0.83[ASN][1000 genomes]
rs3779047	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3800951	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3823646	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4424195	0.89[YRI][hapmap]
rs4729566	0.82[YRI][hapmap]
rs4729567	0.83[YRI][hapmap]
rs7785392	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7787294	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7787492	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7788746	0.82[YRI][hapmap]
rs999885	0.85[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	esv1798486	chr7:99689883-99930879	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1085 gene(s)	inside rSNPs	diseases
4	esv1833059	chr7:99689883-99930879	Flanking Active TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1085 gene(s)	inside rSNPs	diseases
5	esv3350965	chr7:99747460-100146105	Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	304 gene(s)	inside rSNPs	diseases
6	nsv427794	chr7:99750981-99960900	Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
7	nsv428180	chr7:99750981-99960900	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Strong transcription 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	51 gene(s)	inside rSNPs	diseases
8	nsv888773	chr7:99751594-99772298	Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7807641	AP4M1	cis	Artery Tibial	GTEx
rs7807641	TAF6	cis	Thyroid	GTEx
rs7807641	ZKSCAN1	cis	multi-tissue	Pritchard
rs7807641	TAF6	Cis_1M	lymphoblastoid	RTeQTL
rs7807641	AP4M1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:99754800-99757000	Active TSS	HUES64 Cell Line	embryonic stem cell
2	chr7:99755000-99756800	Active TSS	H9 Cell Line	embryonic stem cell
3	chr7:99755200-99756800	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr7:99755200-99756800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
5	chr7:99755200-99756800	Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr7:99755200-99757000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr7:99755400-99756600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr7:99755400-99756600	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
9	chr7:99755400-99756600	Active TSS	Colon Smooth Muscle	Colon
10	chr7:99755400-99756800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr7:99755400-99756800	Active TSS	iPS-20b Cell Line	embryonic stem cell
12	chr7:99755400-99756800	Active TSS	Psoas Muscle	Psoas
13	chr7:99755400-99756800	Active TSS	Right Ventricle	heart
14	chr7:99755600-99756600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
15	chr7:99755600-99756600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr7:99755600-99756600	Active TSS	Breast Myoepithelial Primary Cells	Breast
17	chr7:99755600-99756600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr7:99755600-99756600	Active TSS	Primary T killer memory cells from peripheral blood	blood
19	chr7:99755600-99756600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr7:99755600-99756600	Active TSS	Muscle Satellite Cultured Cells	--
21	chr7:99755600-99756600	Active TSS	Aorta	Aorta
22	chr7:99755600-99756600	Active TSS	Fetal Intestine Large	intestine
23	chr7:99755600-99756600	Active TSS	Fetal Intestine Small	intestine
24	chr7:99755600-99756600	Active TSS	Gastric	stomach
25	chr7:99755600-99756600	Active TSS	Pancreas	Pancrea
26	chr7:99755600-99756600	Active TSS	Hela-S3	cervix
27	chr7:99755600-99756600	Active TSS	HepG2	liver
28	chr7:99755600-99756600	Active TSS	HUVEC	blood vessel
29	chr7:99755600-99756600	Active TSS	K562	blood
30	chr7:99755600-99756600	Active TSS	Osteobl	bone
31	chr7:99755600-99756800	Active TSS	H1 Cell Line	embryonic stem cell
32	chr7:99755600-99756800	Active TSS	HUES48 Cell Line	embryonic stem cell
33	chr7:99755600-99756800	Active TSS	HUES6 Cell Line	embryonic stem cell
34	chr7:99755600-99756800	Active TSS	iPS-15b Cell Line	embryonic stem cell
35	chr7:99755600-99756800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr7:99755600-99756800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr7:99755600-99756800	Active TSS	Brain Angular Gyrus	brain
38	chr7:99755600-99756800	Active TSS	Duodenum Smooth Muscle	Duodenum
39	chr7:99755600-99756800	Active TSS	Esophagus	oesophagus
40	chr7:99755600-99756800	Active TSS	Ovary	ovary
41	chr7:99755600-99756800	Active TSS	Right Atrium	heart
42	chr7:99755600-99756800	Active TSS	Sigmoid Colon	Sigmoid Colon
43	chr7:99755600-99756800	Active TSS	Small Intestine	intestine
44	chr7:99755600-99756800	Active TSS	A549	lung
45	chr7:99755600-99756800	Active TSS	GM12878-XiMat	blood
46	chr7:99755600-99756800	Active TSS	HSMM	muscle
47	chr7:99755600-99757000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr7:99755600-99757000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr7:99755600-99757000	Active TSS	iPS-18 Cell Line	embryonic stem cell
50	chr7:99755600-99757000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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