Variant report

Variant	rs12978479
Chromosome Location	chr19:35659379-35659380
allele	C/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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:35658697..35660776-chr19:35739212..35740943,2	K562	blood:
2	chr19:35653735..35656865-chr19:35656931..35659382,3	MCF-7	breast:
3	chr19:35659165..35661294-chr19:35670153..35671780,2	K562	blood:
4	chr19:35653833..35655711-chr19:35656998..35660022,4	K562	blood:
5	chr19:35658586..35660197-chr19:35739044..35740712,2	K562	blood:
6	chr19:35658538..35660564-chr19:35760467..35762500,2	K562	blood:
7	chr19:35657732..35659414-chr19:35738597..35740391,2	MCF-7	breast:
8	chr19:35658448..35660082-chr19:35706961..35709327,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000105699	Chromatin interaction
ENSG00000089327	Chromatin interaction
ENSG00000105698	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10411557	0.81[ASN][1000 genomes]
rs10419422	0.81[ASN][1000 genomes]
rs10419663	0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs10424450	0.80[ASN][1000 genomes]
rs10425525	0.81[ASN][1000 genomes]
rs11084801	0.97[ASN][1000 genomes]
rs11084802	0.97[ASN][1000 genomes]
rs11084803	0.88[CHB][hapmap];0.81[JPT][hapmap];0.97[ASN][1000 genomes]
rs11882781	0.81[ASN][1000 genomes]
rs12459611	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12609891	0.97[ASN][1000 genomes]
rs12611051	0.88[CHB][hapmap];0.81[JPT][hapmap];0.97[ASN][1000 genomes]
rs12974228	0.80[ASN][1000 genomes]
rs12984052	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2008052	0.81[ASN][1000 genomes]
rs2106447	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2901967	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34197953	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34571941	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3458	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34677175	0.83[ASN][1000 genomes]
rs35436785	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35575880	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35921432	0.83[ASN][1000 genomes]
rs36087337	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4416138	0.80[ASN][1000 genomes]
rs4805111	0.80[ASN][1000 genomes]
rs4806100	0.80[ASN][1000 genomes]
rs56413999	0.81[ASN][1000 genomes]
rs58300983	0.81[ASN][1000 genomes]
rs61192962	0.81[ASN][1000 genomes]
rs71352910	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs8109212	0.80[ASN][1000 genomes]
rs8112633	0.80[ASN][1000 genomes]
rs9304868	0.80[ASN][1000 genomes]
rs9304869	0.80[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	nsv432045	chr19:35556260-36520760	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	nsv911616	chr19:35577870-35669071	Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
3	esv2757694	chr19:35653642-35673333	ZNF genes & repeats Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	esv2758757	chr19:35653642-35673333	Genic enhancers Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv2470	chr19:35655281-35702565	Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Active TSS	Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv1060100	chr19:35658505-36170042	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
7	nsv543993	chr19:35658505-36170042	Enhancers Strong transcription Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
8	esv3395817	chr19:35659112-35663810	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12978479	FXYD5	Cis_1M	lymphoblastoid	RTeQTL
rs12978479	FXYD5	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:35648000-35661600	Strong transcription	H1 Cell Line	embryonic stem cell
2	chr19:35648000-35661800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr19:35648200-35662800	Strong transcription	HUES48 Cell Line	embryonic stem cell
4	chr19:35652000-35661800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
5	chr19:35653400-35663800	Weak transcription	Stomach Mucosa	stomach
6	chr19:35653600-35667400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr19:35653800-35661400	Strong transcription	Primary neutrophils fromperipheralblood	blood
8	chr19:35655200-35667600	Weak transcription	Colonic Mucosa	Colon
9	chr19:35655600-35661400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr19:35657200-35660400	Genic enhancers	Primary T cells fromperipheralblood	blood
11	chr19:35657400-35662200	Weak transcription	Small Intestine	intestine
12	chr19:35657400-35663200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr19:35657600-35659600	Genic enhancers	Primary T helper cells fromperipheralblood	blood
14	chr19:35657600-35660200	Genic enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr19:35657600-35660400	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr19:35657600-35660600	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
17	chr19:35657600-35661800	Strong transcription	HUES64 Cell Line	embryonic stem cell
18	chr19:35657600-35663000	Weak transcription	Duodenum Mucosa	Duodenum
19	chr19:35657600-35666800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr19:35657800-35659400	Strong transcription	ES-I3 Cell Line	embryonic stem cell
21	chr19:35657800-35659400	Enhancers	Primary hematopoietic stem cells	blood
22	chr19:35657800-35659400	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
23	chr19:35657800-35659400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr19:35657800-35659400	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr19:35657800-35659600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr19:35657800-35659600	Genic enhancers	Primary monocytes fromperipheralblood	blood
27	chr19:35657800-35660600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
28	chr19:35657800-35660600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr19:35657800-35661200	Strong transcription	H9 Cell Line	embryonic stem cell
30	chr19:35657800-35661400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr19:35657800-35661800	Strong transcription	HUES6 Cell Line	embryonic stem cell
32	chr19:35657800-35661800	Strong transcription	NHLF	lung
33	chr19:35657800-35662800	Weak transcription	Fetal Intestine Large	intestine
34	chr19:35657800-35663400	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
35	chr19:35657800-35663600	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr19:35657800-35663800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr19:35657800-35666800	Weak transcription	Right Ventricle	heart
38	chr19:35658000-35659400	Weak transcription	Left Ventricle	heart
39	chr19:35658000-35659800	Genic enhancers	HMEC	breast
40	chr19:35658000-35660000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr19:35658000-35660400	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr19:35658000-35660400	Weak transcription	Fetal Intestine Small	intestine
43	chr19:35658000-35660800	Genic enhancers	NHEK	skin
44	chr19:35658000-35661000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr19:35658000-35661600	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr19:35658000-35662600	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr19:35658000-35663600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr19:35658000-35667000	Weak transcription	HSMM	muscle
49	chr19:35658200-35659400	Genic enhancers	Esophagus	oesophagus
50	chr19:35658200-35659400	Strong transcription	A549	lung

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