Variant report

Variant	rs2332655
Chromosome Location	chr4:174093002-174093003
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:174088782-174094458	PANC-1	pancreas:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:173960802..173963006-chr4:174092691..174094595,2	MCF-7	breast:
2	chr4:173946182..173946922-chr4:174091942..174093328,5	MCF-7	breast:
3	chr4:174088223..174092682-chr4:174092972..174099857,11	MCF-7	breast:
4	chr4:174091292..174097320-chr4:174098048..174101316,8	K562	blood:
5	chr4:174026266..174028030-chr4:174092674..174094208,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000245213	TF binding region
ENSG00000245213	Chromatin interaction
ENSG00000109586	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10001613	0.91[TSI][hapmap];0.87[EUR][1000 genomes]
rs10011724	0.96[ASN][1000 genomes]
rs10027708	0.89[ASN][1000 genomes]
rs10031414	0.85[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs1006002	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1006003	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1008052	0.88[CEU][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10213525	0.88[CEU][hapmap];0.80[CHB][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes]
rs1054496	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1054497	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11731263	0.84[EUR][1000 genomes]
rs13112928	0.88[CEU][hapmap];0.87[EUR][1000 genomes]
rs17059221	0.84[CEU][hapmap]
rs1991727	0.94[JPT][hapmap]
rs2332654	0.96[ASN][1000 genomes]
rs2332669	0.94[JPT][hapmap]
rs28377337	0.84[EUR][1000 genomes]
rs28477433	0.85[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs28612521	0.85[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs28663544	0.83[EUR][1000 genomes]
rs3733477	0.97[ASN][1000 genomes]
rs4377567	0.88[ASW][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs4535319	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs4643788	0.80[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs4695826	0.93[ASN][1000 genomes]
rs60815517	0.86[EUR][1000 genomes]
rs6822683	0.84[ASN][1000 genomes]
rs6822875	0.84[ASN][1000 genomes]
rs6835098	0.96[ASN][1000 genomes]
rs6843769	0.84[JPT][hapmap]
rs72711045	0.83[EUR][1000 genomes]
rs7657374	0.82[ASN][1000 genomes]
rs7672108	0.94[JPT][hapmap]
rs9683937	0.84[CEU][hapmap]
rs9685946	0.84[CEU][hapmap];0.84[TSI][hapmap]
rs9990666	0.82[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs9999740	0.89[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	esv1793569	chr4:174090004-174093002	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	esv1793960	chr4:174090004-174102397	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	esv1801469	chr4:174090004-174102397	Enhancers Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	esv1799519	chr4:174090004-174173743	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	esv1823585	chr4:174090209-174107537	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2332655	MORF4	cis	parietal	SCAN
rs2332655	HMGB2	cis	parietal	SCAN

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:174091200-174094000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr4:174091400-174093400	Weak transcription	Lung	lung
3	chr4:174091600-174093200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr4:174091600-174093200	Weak transcription	Spleen	Spleen
5	chr4:174091600-174093400	Weak transcription	Pancreas	Pancrea
6	chr4:174091600-174094200	Enhancers	Primary B cells from peripheral blood	blood
7	chr4:174091600-174094600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr4:174091600-174095000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr4:174091600-174113600	Weak transcription	Esophagus	oesophagus
10	chr4:174091800-174093200	Weak transcription	Fetal Muscle Trunk	muscle
11	chr4:174091800-174093600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr4:174091800-174093600	Enhancers	Fetal Muscle Leg	muscle
13	chr4:174091800-174094600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr4:174091800-174104000	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr4:174092000-174093200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr4:174092000-174093200	Enhancers	Brain Inferior Temporal Lobe	brain
17	chr4:174092000-174093200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr4:174092000-174093400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr4:174092000-174094400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr4:174092000-174095000	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr4:174092000-174096800	Enhancers	ES-I3 Cell Line	embryonic stem cell
22	chr4:174092000-174098600	Weak transcription	Brain Angular Gyrus	brain
23	chr4:174092200-174093200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr4:174092200-174093600	Enhancers	Primary T helper cells PMA-I stimulated	--
25	chr4:174092200-174093600	Enhancers	Brain Anterior Caudate	brain
26	chr4:174092200-174096200	Enhancers	Duodenum Mucosa	Duodenum
27	chr4:174092200-174096400	Enhancers	Stomach Mucosa	stomach
28	chr4:174092200-174098800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
29	chr4:174092200-174099000	Enhancers	H1 Cell Line	embryonic stem cell
30	chr4:174092200-174099000	Enhancers	H9 Cell Line	embryonic stem cell
31	chr4:174092400-174093600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr4:174092400-174094000	Enhancers	Small Intestine	intestine
33	chr4:174092400-174094000	Flanking Active TSS	Thymus	Thymus
34	chr4:174092400-174100400	Weak transcription	Hela-S3	cervix
35	chr4:174092600-174093400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr4:174092600-174093400	Active TSS	Rectal Smooth Muscle	rectum
37	chr4:174092600-174093600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr4:174092600-174093600	Enhancers	Gastric	stomach
39	chr4:174092600-174094800	Weak transcription	Primary T helper cells fromperipheralblood	blood
40	chr4:174092600-174095000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
41	chr4:174092600-174095000	Weak transcription	Brain Hippocampus Middle	brain
42	chr4:174092600-174095000	Weak transcription	Fetal Kidney	kidney
43	chr4:174092600-174095400	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr4:174092600-174096800	Enhancers	Primary hematopoietic stem cells	blood
45	chr4:174092600-174097800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr4:174092600-174099200	Enhancers	HUES48 Cell Line	embryonic stem cell
47	chr4:174092600-174099200	Enhancers	iPS-18 Cell Line	embryonic stem cell
48	chr4:174092600-174102400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr4:174092800-174093200	Enhancers	iPS-20b Cell Line	embryonic stem cell
50	chr4:174092800-174093200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links