Variant report

Variant	rs28534973
Chromosome Location	chr19:18535607-18535608
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:18534926-18553479	K562	blood:	n/a	n/a
2	POLR2A	chr19:18535582-18535630	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr19:18535419-18535734	K562	blood:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:18519965..18521698-chr19:18535153..18537239,2	MCF-7	breast:
2	chr19:18450263..18452147-chr19:18534963..18536741,2	K562	blood:
3	chr19:18534057..18535915-chr19:18572174..18573934,2	MCF-7	breast:
4	chr19:18384108..18395354-chr19:18534355..18544725,18	K562	blood:
5	chr19:18401829..18404172-chr19:18534025..18536659,2	K562	blood:
6	chr19:18534646..18537206-chr19:18547129..18549034,2	MCF-7	breast:
7	chr19:18450604..18452232-chr19:18534647..18536467,2	MCF-7	breast:
8	chr19:18389169..18391132-chr19:18534059..18535898,2	K562	blood:
9	chr19:18534817..18537045-chr19:18704121..18707068,2	MCF-7	breast:
10	chr19:18414113..18417872-chr19:18534099..18536175,3	K562	blood:

No data

Variant related genes	Relation type
SSBP4	TF binding region
ENSG00000130518	Chromatin interaction
ENSG00000130517	Chromatin interaction
ENSG00000105655	Chromatin interaction
ENSG00000130522	Chromatin interaction
ENSG00000221167	Chromatin interaction
ENSG00000006016	Chromatin interaction
ENSG00000267959	Chromatin interaction

Extended variants
information (count: 87 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10402247	0.83[EUR][1000 genomes]
rs10402322	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10409346	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10409408	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10410797	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10413922	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10416993	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10418331	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10418554	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10420384	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10423802	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10426768	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1045631	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11086110	0.95[EUR][1000 genomes]
rs11668704	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11670392	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11672385	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11879757	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12980726	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12982295	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12983263	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1469412	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1469413	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1971093	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2013069	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2162797	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2303692	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2891676	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34213500	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35004712	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35336015	0.83[EUR][1000 genomes]
rs35742476	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4006662	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4303657	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4580317	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4808135	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4808802	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4808803	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4808805	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4808806	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4808807	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4808808	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4808811	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4808812	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4808813	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55715336	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57923655	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6512268	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6512269	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6512270	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6512271	0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7246788	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7247540	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7249760	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7252130	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7252185	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7255936	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7256530	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7258891	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7259135	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7507218	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8100343	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8102717	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8104247	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8106068	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8106332	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8111397	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8111582	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8111824	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8112372	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8112859	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs888668	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs888669	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532614	chr19:18033043-18573963	Flanking Active TSS Enhancers Active TSS Genic enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	204 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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
6	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
7	nsv911275	chr19:18484922-18586759	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	50 gene(s)	inside rSNPs	diseases
8	nsv911276	chr19:18497141-18554972	Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
9	nsv911277	chr19:18520231-18552139	Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
10	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
11	nsv911278	chr19:18526536-18550276	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	39 gene(s)	inside rSNPs	diseases
12	nsv911279	chr19:18533642-18550276	Flanking Active TSS Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	26 gene(s)	inside rSNPs	diseases
13	nsv911280	chr19:18533642-18552139	Genic enhancers Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
14	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs28534973	SSBP4	Cis_1M	lymphoblastoid	RTeQTL
rs28534973	LOC646044///SSBP4	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:18531200-18540000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
2	chr19:18531400-18536400	Weak transcription	Liver	Liver
3	chr19:18531400-18537400	Enhancers	Fetal Thymus	thymus
4	chr19:18531400-18539400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr19:18531400-18539600	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr19:18531400-18539800	Weak transcription	Brain Substantia Nigra	brain
7	chr19:18531400-18543000	Enhancers	Fetal Brain Male	brain
8	chr19:18531800-18537600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr19:18531800-18539600	Genic enhancers	Fetal Stomach	stomach
10	chr19:18532000-18536200	Weak transcription	Gastric	stomach
11	chr19:18532000-18536200	Weak transcription	Rectal Smooth Muscle	rectum
12	chr19:18532000-18536400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr19:18532000-18536400	Weak transcription	NH-A	brain
14	chr19:18532000-18536600	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr19:18532000-18536800	Weak transcription	HMEC	breast
16	chr19:18532000-18537200	Weak transcription	Brain Cingulate Gyrus	brain
17	chr19:18532200-18536400	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr19:18532200-18536400	Weak transcription	Colon Smooth Muscle	Colon
19	chr19:18532200-18536400	Weak transcription	NHEK	skin
20	chr19:18532200-18536800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr19:18532200-18537600	Genic enhancers	Fetal Intestine Small	intestine
22	chr19:18532400-18536200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr19:18532400-18536200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr19:18532400-18536200	Weak transcription	HSMMtube	muscle
25	chr19:18532400-18536400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr19:18532400-18536400	Weak transcription	HSMM	muscle
27	chr19:18532400-18536800	Enhancers	Primary T helper naive cells from peripheral blood	blood
28	chr19:18532400-18538000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
29	chr19:18532400-18538600	Enhancers	Primary T helper cells PMA-I stimulated	--
30	chr19:18532400-18539400	Weak transcription	Primary hematopoietic stem cells	blood
31	chr19:18532400-18539600	Enhancers	Primary T helper cells fromperipheralblood	blood
32	chr19:18532600-18536000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr19:18532600-18536200	Weak transcription	Ovary	ovary
34	chr19:18532600-18536400	Weak transcription	Osteobl	bone
35	chr19:18532600-18536600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr19:18532800-18547600	Weak transcription	HepG2	liver
37	chr19:18533200-18536200	Weak transcription	Pancreas	Pancrea
38	chr19:18533600-18536200	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr19:18533600-18538600	Enhancers	Skeletal Muscle Female	skeletal muscle
40	chr19:18533800-18535800	Enhancers	Primary T cells from cord blood	blood
41	chr19:18533800-18535800	Enhancers	Small Intestine	intestine
42	chr19:18533800-18537800	Enhancers	Left Ventricle	heart
43	chr19:18533800-18538200	Weak transcription	Primary monocytes fromperipheralblood	blood
44	chr19:18533800-18539200	Weak transcription	Monocytes-CD14+_RO01746	blood
45	chr19:18533800-18541000	Enhancers	Placenta	Placenta
46	chr19:18534000-18535800	Enhancers	H1 Cell Line	embryonic stem cell
47	chr19:18534000-18537000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
48	chr19:18534000-18539400	Weak transcription	Primary B cells from cord blood	blood
49	chr19:18534000-18539600	Enhancers	Primary T cells fromperipheralblood	blood
50	chr19:18534000-18539600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--

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