Variant report

Variant	rs8104247
Chromosome Location	chr19:18628205-18628206
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:18627652..18630602-chr19:18688456..18690263,2	K562	blood:
2	chr19:18611587..18620542-chr19:18622883..18629236,13	MCF-7	breast:
3	chr19:18625885..18628372-chr19:18639821..18642383,2	MCF-7	breast:
4	chr19:18624024..18629348-chr19:18653543..18656506,5	K562	blood:
5	chr19:18606497..18609266-chr19:18627874..18630589,2	MCF-7	breast:
6	chr19:18620364..18629414-chr19:18629622..18635316,18	MCF-7	breast:
7	chr19:18625528..18629549-chr19:18629615..18633672,9	K562	blood:

Variant related genes	Relation type
ENSG00000105656	Chromatin interaction
ENSG00000105701	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10402322	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10409346	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10409408	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10410797	0.82[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	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10418331	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10418554	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10420384	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10423802	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10426768	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1045631	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11086110	0.81[EUR][1000 genomes]
rs11668704	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11670392	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11672385	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11879757	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12980726	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	0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1469413	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1971093	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2013069	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2162797	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2303692	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28534973	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2891676	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34213500	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35004712	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35742476	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4006662	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4303657	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4580317	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4808135	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4808802	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4808803	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4808805	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4808806	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4808807	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4808808	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4808811	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4808812	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4808813	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55715336	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57923655	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6512268	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6512269	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6512270	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6512271	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7246788	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7247540	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7249760	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7251232	0.85[EUR][1000 genomes]
rs7252130	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7252185	0.94[AFR][1000 genomes];0.97[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	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7258891	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7259135	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7507218	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8100343	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8102717	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8106068	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8106332	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8111397	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8111582	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8111824	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8112372	0.97[AFR][1000 genomes];0.95[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	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	nsv911282	chr19:18624964-18928480	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
11	nsv911283	chr19:18626732-18689830	Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs8104247	SSBP4	Cis_1M	lymphoblastoid	RTeQTL
rs8104247	LOC646044///SSBP4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:18600400-18630600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr19:18613800-18631000	Weak transcription	Fetal Brain Female	brain
3	chr19:18618800-18630000	Weak transcription	Primary hematopoietic stem cells	blood
4	chr19:18618800-18630800	Weak transcription	Thymus	Thymus
5	chr19:18618800-18631000	Enhancers	Skeletal Muscle Female	skeletal muscle
6	chr19:18620200-18630600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr19:18621600-18630200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr19:18623600-18631000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
9	chr19:18623800-18631000	Enhancers	Fetal Intestine Large	intestine
10	chr19:18624200-18630800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr19:18624400-18630200	Enhancers	Primary T helper cells fromperipheralblood	blood
12	chr19:18625000-18630200	Weak transcription	Rectal Smooth Muscle	rectum
13	chr19:18625600-18628400	Enhancers	Primary T helper naive cells from peripheral blood	blood
14	chr19:18625800-18629000	Enhancers	Spleen	Spleen
15	chr19:18626000-18630800	Weak transcription	Brain Germinal Matrix	brain
16	chr19:18626000-18631200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
17	chr19:18626200-18628400	Enhancers	Primary T helper cells PMA-I stimulated	--
18	chr19:18626200-18629600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr19:18626200-18630400	Enhancers	Skeletal Muscle Male	skeletal muscle
20	chr19:18626200-18630800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr19:18626200-18630800	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr19:18626200-18630800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
23	chr19:18626200-18631000	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr19:18626400-18629800	Weak transcription	Stomach Smooth Muscle	stomach
25	chr19:18626400-18630200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr19:18626400-18630600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr19:18626400-18630800	Weak transcription	Brain Cingulate Gyrus	brain
28	chr19:18626400-18630800	Enhancers	Duodenum Mucosa	Duodenum
29	chr19:18626600-18629600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr19:18626600-18630200	Weak transcription	HSMM	muscle
31	chr19:18626600-18630600	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr19:18626600-18631000	Weak transcription	Ovary	ovary
33	chr19:18626800-18629600	Weak transcription	HMEC	breast
34	chr19:18626800-18629600	Weak transcription	K562	blood
35	chr19:18626800-18629800	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr19:18626800-18630000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr19:18626800-18630000	Weak transcription	Fetal Kidney	kidney
38	chr19:18626800-18630200	Weak transcription	Brain Substantia Nigra	brain
39	chr19:18626800-18630200	Weak transcription	Colon Smooth Muscle	Colon
40	chr19:18626800-18630200	Weak transcription	HUVEC	blood vessel
41	chr19:18626800-18630200	Weak transcription	NH-A	brain
42	chr19:18626800-18630200	Weak transcription	NHDF-Ad	bronchial
43	chr19:18626800-18630600	Weak transcription	Aorta	Aorta
44	chr19:18626800-18630600	Weak transcription	Fetal Lung	lung
45	chr19:18626800-18630800	Weak transcription	Brain Angular Gyrus	brain
46	chr19:18627000-18630600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr19:18627000-18630600	Weak transcription	A549	lung
48	chr19:18627200-18630200	Weak transcription	Stomach Mucosa	stomach
49	chr19:18627200-18630600	Weak transcription	Brain Anterior Caudate	brain
50	chr19:18627200-18630600	Weak transcription	Placenta Amnion	Placenta Amnion

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links