Variant report

Variant	rs11670392
Chromosome Location	chr19:18607780-18607781
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:18606742..18608305-chr19:18615272..18617836,2	MCF-7	breast:
2	chr19:18605488..18607931-chr19:18681544..18684066,2	MCF-7	breast:
3	chr19:18586454..18593275-chr19:18604315..18608580,6	K562	blood:
4	chr19:18606497..18609266-chr19:18627874..18630589,2	MCF-7	breast:
5	chr19:18606523..18611350-chr19:18611496..18616522,8	K562	blood:
6	chr19:18596217..18598374-chr19:18607142..18610008,2	K562	blood:
7	chr19:18607639..18609981-chr19:18628770..18631366,2	K562	blood:

Variant related genes	Relation type
ENSG00000221983	Chromatin interaction
ENSG00000105656	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10164323	0.85[JPT][hapmap]
rs10402322	0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10409346	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10409408	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10410797	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10413922	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10416993	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10418331	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10418554	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10420384	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10423802	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10426768	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1045631	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11086110	0.81[ASW][hapmap];0.88[CEU][hapmap];0.88[CHB][hapmap];0.82[TSI][hapmap];0.86[EUR][1000 genomes]
rs11668704	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11672385	1.00[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];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11879757	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12980726	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12982295	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12983263	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13344313	0.83[CHD][hapmap]
rs1469412	1.00[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];0.95[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1469413	0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1971093	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2013069	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2162797	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2303692	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28534973	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2891676	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34213500	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];0.93[JPT][hapmap];0.84[MEX][hapmap];0.96[TSI][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35004712	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35742476	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4006662	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4303657	0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4580317	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4808135	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.96[TSI][hapmap];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4808802	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4808803	1.00[ASW][hapmap];0.94[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4808805	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4808806	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4808807	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.96[TSI][hapmap];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4808808	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4808811	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4808812	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4808813	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55715336	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57923655	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6512268	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6512269	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6512270	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6512271	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7246788	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7247540	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7249760	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.96[TSI][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7251640	1.00[CHB][hapmap]
rs7252130	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7252185	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7255936	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7256530	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7258891	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.84[GIH][hapmap];0.93[JPT][hapmap];0.80[MEX][hapmap];0.96[TSI][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7259135	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7507218	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8100343	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8102717	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8104247	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8106068	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.96[TSI][hapmap];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8106332	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8111397	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8111582	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8111824	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];0.93[JPT][hapmap];0.84[MEX][hapmap];0.96[TSI][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8112372	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8112859	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs888668	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs888669	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];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]

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	esv3323899	chr19:18343484-18620429	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	162 gene(s)	inside rSNPs	diseases
2	nsv911274	chr19:18440942-18691942	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
3	nsv1057795	chr19:18453362-18883844	Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
4	nsv543925	chr19:18453362-18883844	Weak transcription Genic enhancers Strong transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
5	nsv428018	chr19:18454891-18663981	Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	61 gene(s)	inside rSNPs	diseases
6	nsv1060687	chr19:18522527-18643218	Genic enhancers Strong transcription Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
7	nsv532615	chr19:18534867-18796031	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
8	nsv1061733	chr19:18574940-18679155	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs11670392	ZNF93	cis	cerebellum	SCAN
rs11670392	ISYNA1	cis	parietal	SCAN
rs11670392	SSBP4	cis	lymphoblastoid	seeQTL
rs11670392	LOC646044///SSBP4	Cis_1M	lymphoblastoid	RTeQTL
rs11670392	SSBP4	Cis_1M	lymphoblastoid	RTeQTL
rs11670392	SNORA68	cis	cerebellum	SCAN
rs11670392	ABHD8	cis	parietal	SCAN
rs11670392	CYP4F11	cis	parietal	SCAN
rs11670392	CHERP	cis	cerebellum	SCAN
rs11670392	ZNF14	cis	parietal	SCAN

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:18594000-18621800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
2	chr19:18598000-18609800	Weak transcription	Fetal Intestine Large	intestine
3	chr19:18599400-18611200	Weak transcription	Brain Germinal Matrix	brain
4	chr19:18599800-18611400	Weak transcription	Aorta	Aorta
5	chr19:18600200-18610400	Weak transcription	Brain Substantia Nigra	brain
6	chr19:18600200-18611400	Weak transcription	Rectal Smooth Muscle	rectum
7	chr19:18600400-18609200	Weak transcription	Brain Cingulate Gyrus	brain
8	chr19:18600400-18630600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr19:18600600-18611400	Enhancers	Skeletal Muscle Male	skeletal muscle
10	chr19:18600600-18619800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr19:18602200-18621400	Enhancers	Right Ventricle	heart
12	chr19:18602400-18608600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
13	chr19:18602600-18621400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
14	chr19:18602800-18608200	Enhancers	Left Ventricle	heart
15	chr19:18602800-18608400	Enhancers	Lung	lung
16	chr19:18602800-18612600	Enhancers	Placenta	Placenta
17	chr19:18603000-18608200	Enhancers	Esophagus	oesophagus
18	chr19:18603200-18607800	Enhancers	Stomach Smooth Muscle	stomach
19	chr19:18603600-18607800	Enhancers	Right Atrium	heart
20	chr19:18603600-18608400	Enhancers	HepG2	liver
21	chr19:18603600-18622600	Enhancers	Psoas Muscle	Psoas
22	chr19:18603800-18608000	Enhancers	Adipose Nuclei	Adipose
23	chr19:18603800-18608200	Enhancers	Duodenum Smooth Muscle	Duodenum
24	chr19:18604000-18608400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
25	chr19:18604000-18608600	Enhancers	Liver	Liver
26	chr19:18604000-18608800	Enhancers	Sigmoid Colon	Sigmoid Colon
27	chr19:18604200-18610600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr19:18604200-18619000	Enhancers	Fetal Thymus	thymus
29	chr19:18604400-18607800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
30	chr19:18604400-18607800	Enhancers	Cortex derived primary cultured neurospheres	brain
31	chr19:18604400-18608200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr19:18604400-18608200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
33	chr19:18604400-18608400	Enhancers	Stomach Mucosa	stomach
34	chr19:18604600-18608400	Enhancers	Breast Myoepithelial Primary Cells	Breast
35	chr19:18604800-18607800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr19:18604800-18608200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr19:18604800-18618400	Enhancers	Primary monocytes fromperipheralblood	blood
38	chr19:18605000-18608400	Enhancers	Small Intestine	intestine
39	chr19:18605200-18607800	Enhancers	Rectal Mucosa Donor 29	rectum
40	chr19:18605200-18608200	Enhancers	Primary B cells from peripheral blood	blood
41	chr19:18605200-18608600	Enhancers	Primary T cells from cord blood	blood
42	chr19:18605200-18609000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr19:18605400-18607800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr19:18605400-18607800	Enhancers	Pancreas	Pancrea
45	chr19:18605400-18608400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr19:18605400-18608400	Enhancers	Primary B cells from cord blood	blood
47	chr19:18605400-18608600	Enhancers	GM12878-XiMat	blood
48	chr19:18605400-18621800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
49	chr19:18605600-18608000	Enhancers	NHDF-Ad	bronchial
50	chr19:18605600-18608200	Enhancers	Rectal Mucosa Donor 31	rectum

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