Variant report

Variant	rs2013069
Chromosome Location	chr19:18599757-18599758
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:18596615..18599605-chr19:18599689..18601535,3	K562	blood:
2	chr19:18599219..18600750-chr19:18614089..18616331,2	MCF-7	breast:
3	chr19:18599505..18602337-chr19:18612086..18613638,2	MCF-7	breast:
4	chr19:18597781..18601216-chr19:18667431..18670376,3	MCF-7	breast:
5	chr19:18594286..18597312-chr19:18598721..18600664,3	K562	blood:
6	chr19:18594916..18600646-chr19:18631140..18634129,11	MCF-7	breast:
7	chr19:18597134..18600015-chr19:18874325..18877171,2	MCF-7	breast:
8	chr19:18581749..18584173-chr19:18598767..18601257,2	K562	blood:
9	chr19:18597905..18599605-chr19:18599689..18601535,2	K562	blood:
10	chr19:18594279..18596420-chr19:18597513..18599845,2	MCF-7	breast:
11	chr19:18598368..18601612-chr19:18604293..18607199,5	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000105700	Chromatin interaction
ENSG00000105656	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10164323	0.86[JPT][hapmap]
rs10402322	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10409346	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10409408	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10410797	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10413922	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10416993	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10418331	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10418554	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10420384	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10423802	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10426768	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1045631	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11086110	0.88[CEU][hapmap];0.88[CHB][hapmap];0.81[EUR][1000 genomes]
rs11668704	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11670392	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11672385	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11879757	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12980726	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12982295	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12983263	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1469412	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1469413	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1971093	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2162797	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2303692	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28534973	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2891676	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34213500	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35004712	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35742476	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4006662	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4303657	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4580317	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4808135	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4808802	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4808803	0.94[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4808805	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4808806	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4808807	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4808808	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4808811	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4808812	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4808813	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55715336	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57923655	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6512268	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6512269	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6512270	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6512271	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7246788	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7247540	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7249760	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7251232	0.85[EUR][1000 genomes]
rs7251640	1.00[CHB][hapmap]
rs7252130	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7252185	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7255936	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7256530	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7258891	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7259135	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7507218	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8100343	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8102717	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8104247	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8106068	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8106332	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8111397	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8111582	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8111824	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8112372	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8112859	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs888668	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs888669	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.87[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2013069	LOC646044///SSBP4	Cis_1M	lymphoblastoid	RTeQTL
rs2013069	SSBP4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:18575400-18607200	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr19:18585800-18599800	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr19:18591000-18605400	Weak transcription	Thymus	Thymus
4	chr19:18591400-18605200	Weak transcription	Primary T cells from cord blood	blood
5	chr19:18591400-18605400	Weak transcription	GM12878-XiMat	blood
6	chr19:18593600-18606400	Enhancers	Primary T cells fromperipheralblood	blood
7	chr19:18593800-18601600	Enhancers	Liver	Liver
8	chr19:18594000-18600400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr19:18594000-18601800	Enhancers	Lung	lung
10	chr19:18594000-18605000	Enhancers	Pancreas	Pancrea
11	chr19:18594000-18621800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
12	chr19:18594200-18601600	Enhancers	Placenta	Placenta
13	chr19:18594600-18605600	Weak transcription	Fetal Brain Female	brain
14	chr19:18595200-18600600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
15	chr19:18595200-18600800	Enhancers	Duodenum Smooth Muscle	Duodenum
16	chr19:18595400-18600000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
17	chr19:18595400-18601800	Enhancers	Left Ventricle	heart
18	chr19:18595400-18605800	Enhancers	Primary neutrophils fromperipheralblood	blood
19	chr19:18595600-18600000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr19:18595600-18601600	Enhancers	Psoas Muscle	Psoas
21	chr19:18595600-18601800	Enhancers	Right Ventricle	heart
22	chr19:18595800-18600200	Enhancers	Esophagus	oesophagus
23	chr19:18596000-18601200	Enhancers	Right Atrium	heart
24	chr19:18596000-18601400	Enhancers	Fetal Thymus	thymus
25	chr19:18596200-18599800	Enhancers	Placenta Amnion	Placenta Amnion
26	chr19:18596200-18601200	Enhancers	Brain Anterior Caudate	brain
27	chr19:18596800-18600200	Enhancers	Cortex derived primary cultured neurospheres	brain
28	chr19:18596800-18600200	Enhancers	Brain Inferior Temporal Lobe	brain
29	chr19:18596800-18600200	Enhancers	Brain Substantia Nigra	brain
30	chr19:18596800-18600200	Enhancers	Colon Smooth Muscle	Colon
31	chr19:18597000-18600600	Enhancers	HMEC	breast
32	chr19:18597000-18600800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr19:18597200-18601000	Enhancers	Breast Myoepithelial Primary Cells	Breast
34	chr19:18597200-18601800	Enhancers	Fetal Muscle Leg	muscle
35	chr19:18597400-18599800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr19:18597400-18599800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr19:18597400-18599800	Enhancers	Muscle Satellite Cultured Cells	--
38	chr19:18597400-18600000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr19:18597400-18600200	Enhancers	HSMM	muscle
40	chr19:18597400-18600800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr19:18597400-18603800	Weak transcription	Fetal Kidney	kidney
42	chr19:18597600-18600000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr19:18597600-18600400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr19:18597600-18600400	Enhancers	Brain Cingulate Gyrus	brain
45	chr19:18597600-18600400	Enhancers	Fetal Muscle Trunk	muscle
46	chr19:18597600-18602000	Enhancers	K562	blood
47	chr19:18597600-18606600	Enhancers	Duodenum Mucosa	Duodenum
48	chr19:18597800-18599800	Enhancers	Hela-S3	cervix
49	chr19:18597800-18600000	Enhancers	Brain Angular Gyrus	brain
50	chr19:18597800-18600400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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