Variant report

Variant	rs6512270
Chromosome Location	chr19:18618580-18618581
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:18595683..18597798-chr19:18617038..18618682,2	K562	blood:
2	chr19:18618174..18621109-chr19:18623910..18627140,6	MCF-7	breast:
3	chr19:18618216..18621144-chr19:18680339..18684526,4	K562	blood:
4	chr19:18615807..18618934-chr19:18622122..18624093,3	K562	blood:
5	chr19:18611587..18620542-chr19:18622883..18629236,13	MCF-7	breast:
6	chr19:18616308..18619583-chr19:18680770..18684493,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000221983	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10402322	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10409346	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10409408	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10410797	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10413922	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10416993	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10418331	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10418554	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10420384	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10423802	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10426768	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1045631	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11086110	0.85[EUR][1000 genomes]
rs11668704	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11670392	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11672385	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11879757	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12980726	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12982295	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12983263	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1469412	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1469413	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1971093	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2013069	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2162797	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2303692	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28534973	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2891676	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34213500	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35004712	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35742476	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4006662	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4303657	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4580317	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4808135	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4808802	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4808803	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4808805	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4808806	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4808807	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4808808	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4808811	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4808812	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4808813	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55715336	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57923655	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6512268	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6512269	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6512271	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7246788	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7247540	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7249760	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7252130	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7252185	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7255936	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7256530	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7258891	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7259135	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7507218	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8100343	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8102717	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8104247	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8106068	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8106332	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8111397	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8111582	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8111824	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8112372	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8112859	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs888668	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs888669	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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
9	nsv1055794	chr19:18611545-18676933	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
10	nsv911281	chr19:18613917-18758255	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6512270	LOC646044///SSBP4	Cis_1M	lymphoblastoid	RTeQTL
rs6512270	SSBP4	Cis_1M	lymphoblastoid	RTeQTL
rs6512270	ELL	cis	Whole Blood	GTEx

Chromatin state (count:112 , 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	chr19:18600400-18630600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr19:18600600-18619800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr19:18602200-18621400	Enhancers	Right Ventricle	heart
5	chr19:18602600-18621400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
6	chr19:18603600-18622600	Enhancers	Psoas Muscle	Psoas
7	chr19:18604200-18619000	Enhancers	Fetal Thymus	thymus
8	chr19:18605400-18621800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
9	chr19:18606800-18625800	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr19:18607600-18621600	Enhancers	Primary T killer memory cells from peripheral blood	blood
11	chr19:18607600-18622400	Enhancers	Primary T helper cells fromperipheralblood	blood
12	chr19:18609200-18619600	Enhancers	Duodenum Smooth Muscle	Duodenum
13	chr19:18609200-18620800	Enhancers	Brain Hippocampus Middle	brain
14	chr19:18609200-18621400	Enhancers	Fetal Muscle Trunk	muscle
15	chr19:18609200-18621400	Enhancers	Rectal Mucosa Donor 31	rectum
16	chr19:18609200-18621400	Enhancers	Sigmoid Colon	Sigmoid Colon
17	chr19:18609200-18621600	Enhancers	Liver	Liver
18	chr19:18609200-18621600	Enhancers	Left Ventricle	heart
19	chr19:18609400-18621400	Enhancers	Lung	lung
20	chr19:18609400-18621600	Enhancers	Pancreas	Pancrea
21	chr19:18609800-18620200	Enhancers	Gastric	stomach
22	chr19:18609800-18621000	Enhancers	Fetal Muscle Leg	muscle
23	chr19:18609800-18621400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
24	chr19:18609800-18621800	Enhancers	Right Atrium	heart
25	chr19:18610200-18620800	Enhancers	Fetal Heart	heart
26	chr19:18611000-18620200	Enhancers	Brain Cingulate Gyrus	brain
27	chr19:18611000-18621400	Enhancers	Small Intestine	intestine
28	chr19:18611200-18619400	Enhancers	Esophagus	oesophagus
29	chr19:18611200-18621600	Enhancers	Brain Inferior Temporal Lobe	brain
30	chr19:18611400-18621600	Enhancers	Breast Myoepithelial Primary Cells	Breast
31	chr19:18611800-18619200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr19:18612200-18618600	Enhancers	Primary B cells from peripheral blood	blood
33	chr19:18612400-18620000	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr19:18612600-18619400	Enhancers	Stomach Mucosa	stomach
35	chr19:18613000-18620800	Enhancers	Primary T helper naive cells from peripheral blood	blood
36	chr19:18613000-18621200	Enhancers	Primary hematopoietic stem cells short term culture	blood
37	chr19:18613000-18621400	Enhancers	Placenta	Placenta
38	chr19:18613200-18618600	Enhancers	Spleen	Spleen
39	chr19:18613200-18619200	Enhancers	HSMM	muscle
40	chr19:18613200-18619800	Enhancers	Fetal Intestine Large	intestine
41	chr19:18613400-18618800	Enhancers	Muscle Satellite Cultured Cells	--
42	chr19:18613800-18618800	Enhancers	NHDF-Ad	bronchial
43	chr19:18613800-18620800	Genic enhancers	Fetal Intestine Small	intestine
44	chr19:18613800-18621600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
45	chr19:18613800-18621600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr19:18613800-18631000	Weak transcription	Fetal Brain Female	brain
47	chr19:18614200-18618800	Enhancers	Brain Angular Gyrus	brain
48	chr19:18614200-18621400	Enhancers	Ovary	ovary
49	chr19:18614400-18621000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
50	chr19:18615400-18619200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links