Variant report

Variant	rs1623779
Chromosome Location	chr19:35658188-35658189
allele	A/G
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:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:35657563..35659340-chr19:35750773..35753172,2	K562	blood:
2	chr19:35654052..35658593-chr19:35736953..35742683,9	K562	blood:
3	chr19:35653735..35656865-chr19:35656931..35659382,3	MCF-7	breast:
4	chr19:35606015..35607604-chr19:35656192..35659125,2	MCF-7	breast:
5	chr19:35642928..35645381-chr19:35657672..35659375,2	MCF-7	breast:
6	chr19:35652170..35655595-chr19:35655947..35659208,4	MCF-7	breast:
7	chr19:35653961..35658211-chr19:35756444..35760028,4	K562	blood:
8	chr19:35653833..35655711-chr19:35656998..35660022,4	K562	blood:
9	chr19:35657732..35659414-chr19:35738597..35740391,2	MCF-7	breast:
10	chr19:35656275..35658757-chr19:35668459..35673698,5	K562	blood:
11	chr19:35656896..35658640-chr19:35739040..35741411,2	MCF-7	breast:
12	chr19:35653961..35659020-chr19:35755691..35760689,8	K562	blood:

No data

Variant related genes	Relation type
ENSG00000105699	Chromatin interaction
ENSG00000089356	Chromatin interaction
ENSG00000105698	Chromatin interaction
ENSG00000089327	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs12110	1.00[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.91[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12710029	0.82[EUR][1000 genomes]
rs12975276	0.81[EUR][1000 genomes]
rs1617607	0.94[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1624046	0.87[EUR][1000 genomes]
rs1633915	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1672994	0.85[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1688007	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MKK][hapmap];0.88[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1688008	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1688045	0.82[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2451993	0.85[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.96[MKK][hapmap];0.85[TSI][hapmap];0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs756845	0.82[EUR][1000 genomes]
rs8106303	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs886136	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs1623779	HNRNPUL1	cis	cerebellum	SCAN
rs1623779	GSK3A	cis	cerebellum	SCAN
rs1623779	PPP1R14A	cis	cerebellum	SCAN
rs1623779	LGALS13	cis	parietal	SCAN
rs1623779	ZNF574	cis	parietal	SCAN
rs1623779	HIPK4	cis	parietal	SCAN
rs1623779	AKT2	cis	cerebellum	SCAN
rs1623779	FXYD5	Cis_1M	lymphoblastoid	RTeQTL
rs1623779	FXYD5	cis	lymphoblastoid	seeQTL
rs1623779	ZNF575	cis	parietal	SCAN

Chromatin state (count:97 , 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	chr19:35652200-35658200	ZNF genes & repeats	A549	lung
6	chr19:35652400-35658400	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
7	chr19:35652400-35658400	ZNF genes & repeats	Lung	lung
8	chr19:35652400-35658600	ZNF genes & repeats	Placenta	Placenta
9	chr19:35653400-35663800	Weak transcription	Stomach Mucosa	stomach
10	chr19:35653600-35667400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr19:35653800-35658800	Strong transcription	Dnd41	blood
12	chr19:35653800-35659000	Strong transcription	Placenta Amnion	Placenta Amnion
13	chr19:35653800-35661400	Strong transcription	Primary neutrophils fromperipheralblood	blood
14	chr19:35654800-35658200	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr19:35655000-35658200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
16	chr19:35655200-35667600	Weak transcription	Colonic Mucosa	Colon
17	chr19:35655600-35658800	Strong transcription	NHDF-Ad	bronchial
18	chr19:35655600-35659000	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr19:35655600-35661400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr19:35655800-35658200	Strong transcription	HUVEC	blood vessel
21	chr19:35656200-35658800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr19:35656600-35658200	ZNF genes & repeats	Adipose Nuclei	Adipose
23	chr19:35656600-35658200	ZNF genes & repeats	Esophagus	oesophagus
24	chr19:35656600-35658400	ZNF genes & repeats	Spleen	Spleen
25	chr19:35656800-35658200	Transcr. at gene 5' and 3'	K562	blood
26	chr19:35656800-35658400	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr19:35656800-35658400	ZNF genes & repeats	Fetal Stomach	stomach
28	chr19:35656800-35658800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr19:35657000-35659200	Genic enhancers	Primary B cells from peripheral blood	blood
30	chr19:35657000-35659200	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
31	chr19:35657200-35658200	Strong transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr19:35657200-35658400	Strong transcription	Gastric	stomach
33	chr19:35657200-35658400	Transcr. at gene 5' and 3'	Monocytes-CD14+_RO01746	blood
34	chr19:35657200-35660400	Genic enhancers	Primary T cells fromperipheralblood	blood
35	chr19:35657400-35658200	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
36	chr19:35657400-35658200	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
37	chr19:35657400-35658800	Transcr. at gene 5' and 3'	Primary T cells from cord blood	blood
38	chr19:35657400-35658800	Strong transcription	NH-A	brain
39	chr19:35657400-35659000	Genic enhancers	Primary B cells from cord blood	blood
40	chr19:35657400-35662200	Weak transcription	Small Intestine	intestine
41	chr19:35657400-35663200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr19:35657600-35658200	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
43	chr19:35657600-35658200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr19:35657600-35658800	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
45	chr19:35657600-35659000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr19:35657600-35659600	Genic enhancers	Primary T helper cells fromperipheralblood	blood
47	chr19:35657600-35660200	Genic enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr19:35657600-35660400	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
49	chr19:35657600-35660600	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
50	chr19:35657600-35661800	Strong transcription	HUES64 Cell Line	embryonic stem cell

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