Variant report

Variant	rs6769789
Chromosome Location	chr3:52874446-52874447
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:52803715..52805902-chr3:52874029..52875964,2	MCF-7	breast:
2	chr3:52864085..52867017-chr3:52872869..52875445,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000055955	Chromatin interaction
ENSG00000114904	Chromatin interaction

Extended variants
information (count: 85 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10865977	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11130331	0.87[CEU][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.80[EUR][1000 genomes]
rs11715347	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11719137	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11915546	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11918800	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11922961	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11922975	0.92[CEU][hapmap];0.82[CHD][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap]
rs12487379	0.91[EUR][1000 genomes]
rs12492391	0.96[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap]
rs12638968	0.82[EUR][1000 genomes]
rs13072536	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs13072537	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13083728	0.86[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap]
rs1573815	0.86[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap]
rs2071042	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap]
rs2071044	0.84[YRI][hapmap]
rs2239547	0.86[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap]
rs2239548	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2240915	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2240917	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2245538	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2245647	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2256332	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2276815	0.81[CHB][hapmap];0.90[JPT][hapmap]
rs2276817	0.86[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap]
rs2276823	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2276825	0.86[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap]
rs2336558	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2336664	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2336667	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2336668	0.96[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap];0.83[EUR][1000 genomes]
rs2535633	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3733047	0.86[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap]
rs3774364	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3821873	0.96[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap];0.80[AMR][1000 genomes]
rs4302374	0.85[JPT][hapmap]
rs4350911	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4687554	0.86[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap]
rs4687562	0.81[EUR][1000 genomes]
rs4687657	0.86[CHB][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap]
rs4687658	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs4687663	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs4687672	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs4687679	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4687680	0.96[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap]
rs4687682	0.96[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4687683	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4687684	0.80[AMR][1000 genomes]
rs4687687	0.83[ASW][hapmap];0.92[CEU][hapmap];0.82[CHD][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.89[TSI][hapmap];0.85[YRI][hapmap];0.80[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs4687689	0.81[EUR][1000 genomes]
rs56019197	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56383738	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs60332615	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6445538	0.86[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap]
rs6445539	0.86[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap]
rs6445541	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6445547	0.85[JPT][hapmap]
rs6764322	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6773650	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6795646	0.96[CEU][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];0.85[JPT][hapmap];0.94[MEX][hapmap];0.89[TSI][hapmap]
rs6803519	0.86[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap]
rs736408	0.83[YRI][hapmap]
rs7612624	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7617468	0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7620690	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7626551	0.92[CEU][hapmap]
rs7630552	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7652667	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9682464	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs9810807	0.95[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap]
rs9825230	0.80[EUR][1000 genomes]
rs9836499	0.96[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9850563	0.96[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap];0.84[AMR][1000 genomes]
rs9860296	0.96[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];0.85[JPT][hapmap];0.94[MEX][hapmap];0.89[TSI][hapmap]
rs9866243	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9871175	0.81[EUR][1000 genomes]
rs9876403	0.85[JPT][hapmap]
rs9880619	0.80[EUR][1000 genomes]
rs9880978	0.96[CEU][hapmap];0.91[CHB][hapmap];0.87[CHD][hapmap];0.81[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes]
rs9985365	0.87[CEU][hapmap];0.80[EUR][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	nsv834698	chr3:52749983-52928219	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
2	esv2762328	chr3:52774884-53002150	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	esv3446915	chr3:52786850-53049217	Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv967253	chr3:52871714-52877079	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs6769789	ITIH4-AS1	cis	Artery Aorta	GTEx
rs6769789	SEMA3G	cis	parietal	SCAN
rs6769789	TEX264	cis	parietal	SCAN
rs6769789	GNL3	cis	cerebellum	SCAN
rs6769789	GNL3	cis	parietal	SCAN
rs6769789	GLYCTK	cis	parietal	SCAN
rs6769789	NT5DC2	Cis_1M	lymphoblastoid	RTeQTL
rs6769789	RFT1	cis	cerebellum	SCAN
rs6769789	WDR6	cis	cerebellum	SCAN
rs6769789	ITIH4	cis	lymphoblastoid	seeQTL
rs6769789	ITIH4-AS1	cis	Artery Tibial	GTEx
rs6769789	ITIH4	cis	cerebellum	SCAN

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52854800-52888400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr3:52856000-52875000	Weak transcription	Fetal Intestine Large	intestine
3	chr3:52862000-52882600	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr3:52864400-52875800	Strong transcription	Primary neutrophils fromperipheralblood	blood
5	chr3:52865600-52875200	Weak transcription	Dnd41	blood
6	chr3:52865800-52878600	Weak transcription	Small Intestine	intestine
7	chr3:52866000-52884800	Weak transcription	HMEC	breast
8	chr3:52866200-52885200	Weak transcription	NHEK	skin
9	chr3:52866600-52879200	Weak transcription	Osteobl	bone
10	chr3:52866800-52876400	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr3:52866800-52878200	Strong transcription	Fetal Brain Female	brain
12	chr3:52866800-52879600	Genic enhancers	Fetal Thymus	thymus
13	chr3:52867000-52876400	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr3:52867000-52881600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr3:52867000-52881800	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr3:52867200-52875200	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr3:52868000-52878800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr3:52868000-52883200	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr3:52868400-52877800	Strong transcription	Brain Germinal Matrix	brain
20	chr3:52868600-52875200	Weak transcription	Primary hematopoietic stem cells	blood
21	chr3:52868800-52876800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr3:52869000-52878800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr3:52869000-52879400	Strong transcription	Fetal Intestine Small	intestine
24	chr3:52869000-52881800	Weak transcription	Fetal Kidney	kidney
25	chr3:52869400-52875200	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr3:52869400-52875600	Weak transcription	Colonic Mucosa	Colon
27	chr3:52869600-52875000	Strong transcription	Brain Angular Gyrus	brain
28	chr3:52869600-52875200	Strong transcription	Brain Inferior Temporal Lobe	brain
29	chr3:52869600-52878600	Weak transcription	NHDF-Ad	bronchial
30	chr3:52869600-52879600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr3:52869600-52881800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr3:52869800-52875600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr3:52869800-52876600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr3:52869800-52882000	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr3:52869800-52884000	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr3:52870000-52875000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr3:52870000-52878800	Genic enhancers	Fetal Muscle Leg	muscle
38	chr3:52870000-52901000	Weak transcription	Fetal Brain Male	brain
39	chr3:52870200-52875600	Strong transcription	Stomach Smooth Muscle	stomach
40	chr3:52870200-52876600	Strong transcription	Fetal Stomach	stomach
41	chr3:52870400-52875800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
42	chr3:52870400-52876400	Strong transcription	Duodenum Smooth Muscle	Duodenum
43	chr3:52870400-52877400	Strong transcription	Lung	lung
44	chr3:52870600-52875000	Weak transcription	Primary B cells from peripheral blood	blood
45	chr3:52870600-52875200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr3:52870600-52877000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr3:52870600-52877400	Strong transcription	Adipose Nuclei	Adipose
48	chr3:52870600-52879400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr3:52871000-52875000	Weak transcription	HSMM	muscle
50	chr3:52871200-52875000	Weak transcription	HUES6 Cell Line	embryonic stem cell

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