Variant report

Variant	rs7127090
Chromosome Location	chr11:67891289-67891290
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:67891248-67891431	HepG2	liver:	n/a	n/a
2	MAFF	chr11:67891278-67891526	HepG2	liver:	n/a	chr11:67891431-67891449

No.	Distal block	Cell Line	Cell type
1	chr11:67851371..67853952-chr11:67890361..67892182,2	MCF-7	breast:
2	chr11:67883153..67885077-chr11:67890088..67891678,2	MCF-7	breast:
3	chr11:67809464..67811136-chr11:67889799..67892017,2	K562	blood:
4	chr11:67770998..67775364-chr11:67887455..67891345,5	MCF-7	breast:

Variant related genes	Relation type
CHKA	TF binding region
ENSG00000110057	Chromatin interaction
ENSG00000110719	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10791958	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10896289	0.82[GIH][hapmap]
rs2511439	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2511474	0.85[EUR][1000 genomes]
rs3763945	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4337046	0.92[EUR][1000 genomes]
rs72926470	0.86[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	nsv427892	chr11:67451649-67926562	Bivalent Enhancer Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	116 gene(s)	inside rSNPs	diseases
2	esv2757450	chr11:67472905-67891289	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	112 gene(s)	inside rSNPs	diseases
3	esv2759835	chr11:67472905-67891289	Strong transcription Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	112 gene(s)	inside rSNPs	diseases
4	nsv825963	chr11:67763676-68197054	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	149 gene(s)	inside rSNPs	diseases
5	nsv371	chr11:67881973-67891493	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7127090	SPDYC	cis	parietal	SCAN
rs7127090	KCNK4	cis	cerebellum	SCAN

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:67889400-67891400	Flanking Active TSS	Hela-S3	cervix
2	chr11:67889600-67892000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr11:67889600-67897400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
4	chr11:67889800-67892200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr11:67889800-67892200	Weak transcription	Gastric	stomach
6	chr11:67889800-67892400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr11:67889800-67894600	Weak transcription	Lung	lung
8	chr11:67889800-67895200	Weak transcription	Esophagus	oesophagus
9	chr11:67889800-67895200	Weak transcription	Right Atrium	heart
10	chr11:67889800-67895200	Weak transcription	NH-A	brain
11	chr11:67889800-67895400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr11:67889800-67895400	Weak transcription	Brain Germinal Matrix	brain
13	chr11:67889800-67895400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
14	chr11:67889800-67895400	Enhancers	Placenta	Placenta
15	chr11:67889800-67895400	Weak transcription	Ovary	ovary
16	chr11:67889800-67897400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr11:67889800-67897600	Enhancers	H1 Cell Line	embryonic stem cell
18	chr11:67890000-67891400	Weak transcription	Pancreas	Pancrea
19	chr11:67890000-67891600	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr11:67890000-67892000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr11:67890000-67892000	Enhancers	Rectal Mucosa Donor 29	rectum
22	chr11:67890000-67892600	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr11:67890000-67892800	Enhancers	A549	lung
24	chr11:67890000-67893000	Enhancers	Rectal Mucosa Donor 31	rectum
25	chr11:67890000-67893400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr11:67890000-67893800	Weak transcription	Primary neutrophils fromperipheralblood	blood
27	chr11:67890000-67894200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr11:67890000-67894200	Weak transcription	Adipose Nuclei	Adipose
29	chr11:67890000-67894400	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr11:67890000-67894600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr11:67890000-67894800	Weak transcription	Primary B cells from cord blood	blood
32	chr11:67890000-67894800	Weak transcription	Stomach Smooth Muscle	stomach
33	chr11:67890000-67895200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr11:67890000-67895200	Enhancers	Liver	Liver
35	chr11:67890000-67895200	Weak transcription	Brain Anterior Caudate	brain
36	chr11:67890000-67895200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr11:67890000-67895200	Weak transcription	Colonic Mucosa	Colon
38	chr11:67890000-67895200	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr11:67890000-67895200	Enhancers	Fetal Intestine Large	intestine
40	chr11:67890000-67895400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr11:67890000-67895400	Weak transcription	Primary hematopoietic stem cells	blood
42	chr11:67890000-67895400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr11:67890000-67895400	Weak transcription	Brain Cingulate Gyrus	brain
44	chr11:67890000-67895400	Weak transcription	Brain Hippocampus Middle	brain
45	chr11:67890000-67895400	Weak transcription	Fetal Brain Male	brain
46	chr11:67890000-67895400	Enhancers	Fetal Intestine Small	intestine
47	chr11:67890000-67895400	Weak transcription	HUVEC	blood vessel
48	chr11:67890000-67895400	Weak transcription	K562	blood
49	chr11:67890000-67896000	Weak transcription	Brain Substantia Nigra	brain
50	chr11:67890000-67896200	Weak transcription	Fetal Kidney	kidney

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links