Variant report

Variant	rs11935226
Chromosome Location	chr4:88342150-88342151
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:88341808-88344299	GM12878	blood:	n/a	n/a
2	POLR2A	chr4:88341803-88342727	K562	blood:	n/a	n/a
3	POLR2A	chr4:88341921-88342844	MCF10A-Er-Src	breast:	n/a	n/a
4	POLR2A	chr4:88342052-88344383	GM12891	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:88341987..88343662-chr4:88383872..88386006,2	MCF-7	breast:
2	chr4:88340563..88342774-chr4:88344260..88346848,4	MCF-7	breast:
3	chr4:88340622..88342394-chr4:88382444..88384320,2	MCF-7	breast:
4	chr4:88341784..88343437-chr4:88384944..88387219,2	K562	blood:
5	chr4:88333084..88334930-chr4:88342115..88343742,2	MCF-7	breast:
6	chr4:88339085..88341655-chr4:88342092..88343723,2	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HSD17B11-2	chr4:88341428-88343734	NONHSAT097311

No data

Variant related genes	Relation type
NUDT9	TF binding region
ENSG00000251716	Chromatin interaction
ENSG00000272856	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11932891	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11932933	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11936273	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11937770	0.85[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11940597	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs56189054	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56253808	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58555412	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60350615	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60465726	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60622737	1.00[AFR][1000 genomes]
rs6825532	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6826257	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6833270	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6833835	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6838776	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6839314	0.83[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72877349	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72877357	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72877358	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1004518	chr4:88218473-88354403	Weak transcription Active TSS Genic enhancers Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	nsv1002789	chr4:88239340-88606485	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:88329600-88342600	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr4:88334600-88342800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr4:88339400-88343000	Enhancers	Fetal Intestine Large	intestine
4	chr4:88340000-88343000	Enhancers	Fetal Intestine Small	intestine
5	chr4:88340000-88343000	Enhancers	Pancreas	Pancrea
6	chr4:88340400-88343000	Enhancers	Duodenum Mucosa	Duodenum
7	chr4:88340600-88342600	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr4:88340600-88342600	Enhancers	iPS-15b Cell Line	embryonic stem cell
9	chr4:88340800-88342200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr4:88340800-88342400	Enhancers	iPS-18 Cell Line	embryonic stem cell
11	chr4:88340800-88342400	Enhancers	iPS-20b Cell Line	embryonic stem cell
12	chr4:88340800-88342600	Enhancers	H1 Cell Line	embryonic stem cell
13	chr4:88340800-88342600	Enhancers	HUES6 Cell Line	embryonic stem cell
14	chr4:88340800-88342600	Enhancers	HUES64 Cell Line	embryonic stem cell
15	chr4:88340800-88342600	Enhancers	Fetal Kidney	kidney
16	chr4:88340800-88342800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr4:88340800-88343000	Weak transcription	Colonic Mucosa	Colon
18	chr4:88340800-88343200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr4:88340800-88343200	Weak transcription	Gastric	stomach
20	chr4:88341000-88343000	Enhancers	Rectal Mucosa Donor 31	rectum
21	chr4:88341200-88342400	Enhancers	ES-I3 Cell Line	embryonic stem cell
22	chr4:88341200-88342400	Flanking Active TSS	HepG2	liver
23	chr4:88341200-88342800	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr4:88341200-88343000	Weak transcription	Right Atrium	heart
25	chr4:88341400-88342200	Enhancers	Liver	Liver
26	chr4:88341400-88342200	Enhancers	A549	lung
27	chr4:88341400-88342400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr4:88341400-88342800	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr4:88341400-88343000	Weak transcription	HUVEC	blood vessel
30	chr4:88341400-88343400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
31	chr4:88341600-88342600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr4:88341600-88342600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr4:88341600-88342800	Weak transcription	Psoas Muscle	Psoas
34	chr4:88341600-88343000	Weak transcription	NH-A	brain
35	chr4:88341800-88342800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr4:88341800-88343200	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr4:88341800-88343200	Weak transcription	Small Intestine	intestine
38	chr4:88342000-88342600	Enhancers	GM12878-XiMat	blood
39	chr4:88342000-88343000	Weak transcription	Stomach Mucosa	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links