Variant report

Variant	rs735
Chromosome Location	chr3:113054308-113054309
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 73 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10511325	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs11914782	1.00[MEX][hapmap]
rs11917149	0.91[EUR][1000 genomes]
rs11917288	0.91[EUR][1000 genomes]
rs11919031	1.00[MEX][hapmap]
rs11919330	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs11920725	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs11922838	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11923128	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs11924109	0.91[EUR][1000 genomes]
rs11926687	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs11929418	1.00[MEX][hapmap]
rs1463639	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs1463641	1.00[MEX][hapmap]
rs16845106	0.91[JPT][hapmap]
rs16845109	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs16860709	1.00[TSI][hapmap]
rs16860770	1.00[AFR][1000 genomes]
rs16860847	1.00[MEX][hapmap]
rs16860962	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs16861014	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[EUR][1000 genomes]
rs16861023	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs16861025	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs16861032	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs16861045	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[EUR][1000 genomes]
rs16861077	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs16861109	1.00[CEU][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17255950	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17256551	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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17256752	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17320040	1.00[AFR][1000 genomes]
rs17322613	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1906141	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs1989359	1.00[CEU][hapmap];0.83[JPT][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2129431	0.91[EUR][1000 genomes]
rs2129432	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2291412	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2306068	1.00[CEU][hapmap];0.82[JPT][hapmap];0.91[EUR][1000 genomes]
rs2306070	1.00[CEU][hapmap];0.82[JPT][hapmap];0.91[EUR][1000 genomes]
rs28472841	0.84[EUR][1000 genomes]
rs34600669	1.00[AFR][1000 genomes]
rs35758075	0.91[EUR][1000 genomes]
rs35812463	0.91[EUR][1000 genomes]
rs3732807	1.00[MEX][hapmap]
rs3732808	1.00[MEX][hapmap]
rs3732810	1.00[MEX][hapmap]
rs3814399	0.92[JPT][hapmap]
rs41271353	1.00[AFR][1000 genomes]
rs56685963	0.91[EUR][1000 genomes]
rs56772417	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs57104308	1.00[AFR][1000 genomes]
rs57115529	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs57164268	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs58905600	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs58988763	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs59271111	0.91[EUR][1000 genomes]
rs59493419	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs59673391	0.91[EUR][1000 genomes]
rs59742486	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60582065	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60697865	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60940543	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs61065093	0.91[EUR][1000 genomes]
rs61594119	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6783691	1.00[CEU][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.91[EUR][1000 genomes]
rs7635203	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7636986	1.00[MEX][hapmap]
rs7650500	1.00[MEX][hapmap]
rs7650771	1.00[MEX][hapmap]
rs998647	1.00[AFR][1000 genomes]
rs999365	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3431441	chr3:112453467-113213252	Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv1013506	chr3:112890608-113680951	Weak transcription Bivalent/Poised TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs735	GRAMD1C	cis	lymphoblastoid	seeQTL

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:113013600-113065200	Weak transcription	Left Ventricle	heart
2	chr3:113024600-113081000	Weak transcription	Stomach Smooth Muscle	stomach
3	chr3:113036400-113055600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr3:113036600-113081000	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr3:113036800-113065600	Weak transcription	Aorta	Aorta
6	chr3:113036800-113073600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr3:113036800-113081000	Weak transcription	Gastric	stomach
8	chr3:113036800-113088600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr3:113037800-113065600	Weak transcription	HSMM	muscle
10	chr3:113042000-113080800	Weak transcription	Ovary	ovary
11	chr3:113042200-113116800	Weak transcription	Primary B cells from cord blood	blood
12	chr3:113042400-113059800	Weak transcription	Pancreas	Pancrea
13	chr3:113042400-113103600	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr3:113043800-113065600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr3:113045400-113055400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr3:113045400-113097600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr3:113045600-113073000	Weak transcription	A549	lung
18	chr3:113049400-113068400	Weak transcription	Hela-S3	cervix
19	chr3:113049600-113061000	Weak transcription	Primary hematopoietic stem cells	blood
20	chr3:113050000-113055600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr3:113050200-113065000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr3:113050200-113073000	Weak transcription	Primary T cells from cord blood	blood
23	chr3:113050400-113061800	Weak transcription	Fetal Intestine Small	intestine
24	chr3:113050600-113065000	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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