Variant report

Variant	rs271624
Chromosome Location	chr19:18627953-18627954
allele	A/G
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
ENSG00000105701	Chromatin interaction
ENSG00000105656	Chromatin interaction

Extended variants
information (count: 88 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10164319	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10164323	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10403249	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10405479	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10405636	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10408290	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10409003	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10409483	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10409505	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10411009	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10413237	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10419404	0.85[ASN][1000 genomes]
rs10420384	0.82[JPT][hapmap]
rs10425982	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10427083	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1043327	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10442	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11673604	1.00[CEU][hapmap];0.88[JPT][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12162221	0.91[ASN][1000 genomes]
rs12162223	0.89[ASN][1000 genomes]
rs12981981	0.91[ASN][1000 genomes]
rs1560118	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1560119	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs172032	0.91[ASN][1000 genomes]
rs1806980	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2007981	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2278238	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2288428	0.86[ASN][1000 genomes]
rs2303695	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2303696	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2303697	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2385088	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2385089	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs271621	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs271622	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs271623	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs271626	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs271628	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs271629	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28572537	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34010330	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34053595	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34171762	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34256197	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34746918	0.86[ASN][1000 genomes]
rs3810429	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4595905	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4808133	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4808134	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4808136	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4808801	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4808804	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62121135	0.91[ASN][1000 genomes]
rs7249020	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7251653	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7252707	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7252848	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7253990	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7254249	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7256534	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7257932	0.96[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs7258465	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs748609	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs76194	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs76195	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8100767	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8103622	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8103660	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8105994	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8106096	0.88[ASN][1000 genomes]
rs8107347	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8107351	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8107367	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8107743	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8109573	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8111708	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs875396	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs271624	SSBP4	cis	Esophagus Mucosa	GTEx

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	chr19:18623400-18628000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
9	chr19:18623600-18628000	Enhancers	Fetal Heart	heart
10	chr19:18623600-18631000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr19:18623800-18628200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr19:18623800-18628200	Enhancers	Liver	Liver
13	chr19:18623800-18631000	Enhancers	Fetal Intestine Large	intestine
14	chr19:18624200-18628000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
15	chr19:18624200-18630800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr19:18624400-18630200	Enhancers	Primary T helper cells fromperipheralblood	blood
17	chr19:18624600-18628000	Genic enhancers	Fetal Intestine Small	intestine
18	chr19:18624800-18628000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
19	chr19:18624800-18628000	Enhancers	Esophagus	oesophagus
20	chr19:18624800-18628000	Enhancers	Lung	lung
21	chr19:18624800-18628000	Enhancers	Small Intestine	intestine
22	chr19:18624800-18628200	Enhancers	Primary monocytes fromperipheralblood	blood
23	chr19:18625000-18630200	Weak transcription	Rectal Smooth Muscle	rectum
24	chr19:18625400-18628000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr19:18625400-18628000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr19:18625400-18628000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr19:18625400-18628000	Enhancers	Pancreas	Pancrea
28	chr19:18625400-18628000	Genic enhancers	NHEK	skin
29	chr19:18625400-18628200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr19:18625600-18628000	Genic enhancers	Fetal Muscle Leg	muscle
31	chr19:18625600-18628400	Enhancers	Primary T helper naive cells from peripheral blood	blood
32	chr19:18625800-18628000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
33	chr19:18625800-18628000	Enhancers	Colonic Mucosa	Colon
34	chr19:18625800-18629000	Enhancers	Spleen	Spleen
35	chr19:18626000-18628000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr19:18626000-18628000	Enhancers	Right Ventricle	heart
37	chr19:18626000-18630800	Weak transcription	Brain Germinal Matrix	brain
38	chr19:18626000-18631200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
39	chr19:18626200-18628000	Enhancers	Adipose Nuclei	Adipose
40	chr19:18626200-18628000	Enhancers	Duodenum Smooth Muscle	Duodenum
41	chr19:18626200-18628000	Enhancers	Gastric	stomach
42	chr19:18626200-18628400	Enhancers	Primary T helper cells PMA-I stimulated	--
43	chr19:18626200-18629600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr19:18626200-18630400	Enhancers	Skeletal Muscle Male	skeletal muscle
45	chr19:18626200-18630800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr19:18626200-18630800	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr19:18626200-18630800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
48	chr19:18626200-18631000	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr19:18626400-18628000	Enhancers	Rectal Mucosa Donor 29	rectum
50	chr19:18626400-18628000	Flanking Active TSS	HepG2	liver

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