Variant report

Variant	rs1076235
Chromosome Location	chr19:18775077-18775078
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:18773859..18776430-chr19:18779789..18781984,4	MCF-7	breast:
2	chr19:18767525..18769068-chr19:18774852..18777736,2	K562	blood:
3	chr19:18771428..18776633-chr19:18776726..18782954,6	K562	blood:
4	chr19:18745205..18747948-chr19:18774512..18776512,2	K562	blood:
5	chr19:18759533..18761540-chr19:18773488..18775282,2	K562	blood:
6	chr19:18773178..18776512-chr19:18778910..18781378,3	K562	blood:

Variant related genes	Relation type
ENSG00000167487	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10402536	0.96[CEU][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10403231	1.00[CEU][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10423102	0.84[CEU][hapmap]
rs10423271	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10423676	1.00[CEU][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1076234	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11085237	1.00[CEU][hapmap];0.88[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11085239	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11668617	1.00[CEU][hapmap];0.93[GIH][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12052075	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12610845	1.00[ASW][hapmap];0.96[CEU][hapmap];0.98[GIH][hapmap];0.96[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12974161	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12980154	0.84[CEU][hapmap]
rs12983476	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1473115	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2014914	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3795026	0.84[ASW][hapmap];0.96[CEU][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4808146	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4808841	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4808842	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs71332133	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs889362	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs889363	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][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	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
2	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
3	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
4	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
5	nsv833776	chr19:18638028-18782264	Flanking Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
6	nsv911286	chr19:18652844-18811112	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
7	nsv911289	chr19:18700047-18811112	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
8	esv1849639	chr19:18747006-18780799	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	esv1811733	chr19:18764320-18780799	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	esv1845237	chr19:18764320-18780799	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1076235	CRTC1	cis	cerebellum	SCAN
rs1076235	KLHL26	cis	multi-tissue	Pritchard

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:18749200-18778400	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr19:18756400-18778400	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr19:18759400-18776200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr19:18759800-18778400	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr19:18760400-18794800	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr19:18760800-18776200	Weak transcription	Liver	Liver
7	chr19:18760800-18778400	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr19:18762600-18775600	Weak transcription	Dnd41	blood
9	chr19:18763000-18778400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr19:18767400-18776200	Weak transcription	Pancreas	Pancrea
11	chr19:18767400-18778400	Weak transcription	Aorta	Aorta
12	chr19:18768200-18778600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr19:18768400-18776200	Weak transcription	Rectal Smooth Muscle	rectum
14	chr19:18768600-18778400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr19:18768600-18778400	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr19:18769000-18778400	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr19:18769400-18776400	Weak transcription	Ovary	ovary
18	chr19:18769800-18781000	Weak transcription	Small Intestine	intestine
19	chr19:18770200-18776200	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr19:18770200-18778800	Weak transcription	Fetal Lung	lung
21	chr19:18770400-18778400	Weak transcription	Brain Substantia Nigra	brain
22	chr19:18770400-18793600	Weak transcription	GM12878-XiMat	blood
23	chr19:18770600-18776200	Weak transcription	Duodenum Mucosa	Duodenum
24	chr19:18770800-18775200	Weak transcription	Primary monocytes fromperipheralblood	blood
25	chr19:18770800-18776800	Weak transcription	Left Ventricle	heart
26	chr19:18770800-18783200	Weak transcription	Stomach Mucosa	stomach
27	chr19:18771200-18776000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr19:18771200-18776200	Weak transcription	Esophagus	oesophagus
29	chr19:18771600-18783400	Weak transcription	HUVEC	blood vessel
30	chr19:18771800-18788200	Weak transcription	K562	blood
31	chr19:18772000-18775200	Enhancers	Muscle Satellite Cultured Cells	--
32	chr19:18772000-18776200	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr19:18772000-18777000	Weak transcription	Right Atrium	heart
34	chr19:18772000-18778200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr19:18772000-18778200	Weak transcription	Colonic Mucosa	Colon
36	chr19:18772000-18778600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr19:18772400-18778200	Weak transcription	NHLF	lung
38	chr19:18772600-18775400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr19:18772600-18778400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr19:18773000-18775400	Enhancers	Placenta	Placenta
41	chr19:18773200-18788000	Weak transcription	NHEK	skin
42	chr19:18773400-18775400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr19:18773400-18775800	Enhancers	Fetal Muscle Leg	muscle
44	chr19:18773400-18778000	Genic enhancers	Fetal Stomach	stomach
45	chr19:18773600-18775200	Enhancers	Fetal Heart	heart
46	chr19:18773600-18777000	Weak transcription	Brain Angular Gyrus	brain
47	chr19:18773800-18775400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr19:18773800-18775400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
49	chr19:18773800-18776600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr19:18773800-18778400	Weak transcription	Primary neutrophils fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links