Variant report

Variant	rs2172614
Chromosome Location	chr15:57825607-57825608
allele	C/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	chr15:57825500-57825981	H1-neurons	neurons:	n/a	n/a
2	POLR2A	chr15:57825508-57825958	H1-neurons	neurons:	n/a	n/a
3	REST	chr15:57825477-57825978	H1-neurons	neurons:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:57819966..57822646-chr15:57824885..57827415,2	K562	blood:
2	chr15:57817814..57821842-chr15:57824294..57827570,5	K562	blood:
3	chr15:57817814..57819834-chr15:57824294..57826002,2	K562	blood:

Variant related genes	Relation type
ENSG00000261265	TF binding region
ENSG00000261265	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10220805	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10518923	0.92[TSI][hapmap]
rs10775165	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10851614	0.92[TSI][hapmap]
rs10851615	0.83[AMR][1000 genomes]
rs10851616	0.86[AMR][1000 genomes]
rs10851617	0.83[AMR][1000 genomes]
rs11071323	0.92[TSI][hapmap]
rs11071324	0.86[AMR][1000 genomes]
rs11071325	0.86[AMR][1000 genomes]
rs11071326	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11630712	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11630713	0.81[CHB][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11630740	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11634739	0.85[MEX][hapmap];0.92[TSI][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12323972	0.86[AMR][1000 genomes]
rs12437888	0.92[TSI][hapmap]
rs12439099	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12439126	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12591696	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12593650	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12593685	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12595135	0.92[TSI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12595169	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1319900	0.91[CHB][hapmap];0.89[JPT][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1666567	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16977558	0.88[TSI][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs16977560	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs16977561	0.85[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs16977567	0.85[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];0.96[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs16977585	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.82[TSI][hapmap];0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1980048	0.82[CHB][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1994888	0.92[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1994889	0.92[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2131740	0.92[TSI][hapmap]
rs2172607	0.91[CHB][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2172613	0.85[MEX][hapmap];0.92[TSI][hapmap];0.86[AMR][1000 genomes]
rs2414510	0.83[AMR][1000 genomes]
rs2414511	0.89[ASN][1000 genomes]
rs2942043	0.92[TSI][hapmap]
rs34947057	0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs35709805	0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4545749	0.85[AMR][1000 genomes]
rs55653578	0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs57900088	0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7164486	0.85[MEX][hapmap];0.92[TSI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7182268	0.91[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];0.81[TSI][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7496403	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs878425	0.84[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs932028	0.92[TSI][hapmap]
rs932029	0.84[TSI][hapmap]
rs9806311	0.93[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045611	chr15:57350965-58070807	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv1054547	chr15:57600488-57977659	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv833022	chr15:57657412-57830112	Weak transcription Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv904255	chr15:57790436-57907574	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57797000-57827200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr15:57802600-57846600	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr15:57803200-57842800	Weak transcription	Aorta	Aorta
4	chr15:57811000-57827800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr15:57817000-57826600	Weak transcription	Lung	lung
6	chr15:57817200-57827800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr15:57819200-57841000	Weak transcription	Esophagus	oesophagus
8	chr15:57819800-57826200	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr15:57819800-57826400	Strong transcription	H1 Cell Line	embryonic stem cell
10	chr15:57819800-57829200	Weak transcription	Ovary	ovary
11	chr15:57819800-57833000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr15:57819800-57840000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr15:57820000-57825800	Weak transcription	Fetal Muscle Leg	muscle
14	chr15:57820000-57826600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr15:57820000-57826800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
16	chr15:57820200-57825800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr15:57820200-57829200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr15:57820200-57829400	Weak transcription	Brain Angular Gyrus	brain
19	chr15:57820600-57834000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr15:57820800-57826200	Strong transcription	HUES48 Cell Line	embryonic stem cell
21	chr15:57821600-57825800	Weak transcription	Adipose Nuclei	Adipose
22	chr15:57821800-57842800	Strong transcription	Liver	Liver
23	chr15:57822400-57829000	Weak transcription	Gastric	stomach
24	chr15:57822600-57829200	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr15:57822800-57826600	Weak transcription	HUVEC	blood vessel
26	chr15:57822800-57833000	Weak transcription	HepG2	liver
27	chr15:57822800-57834000	Weak transcription	Colon Smooth Muscle	Colon
28	chr15:57823000-57827600	Enhancers	Fetal Heart	heart
29	chr15:57823000-57828800	Weak transcription	Pancreas	Pancrea
30	chr15:57823600-57828800	Weak transcription	HSMMtube	muscle
31	chr15:57824000-57826400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr15:57824400-57827200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
33	chr15:57824400-57827600	Enhancers	Fetal Lung	lung
34	chr15:57824600-57825800	Strong transcription	H9 Cell Line	embryonic stem cell
35	chr15:57824600-57826000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
36	chr15:57824600-57827000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr15:57824800-57827400	Enhancers	Brain Anterior Caudate	brain
38	chr15:57824800-57827400	Enhancers	Placenta	Placenta
39	chr15:57825000-57826200	Enhancers	Brain Substantia Nigra	brain
40	chr15:57825000-57826200	Genic enhancers	Fetal Stomach	stomach
41	chr15:57825000-57826800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr15:57825000-57827000	Enhancers	Brain Hippocampus Middle	brain
43	chr15:57825000-57827200	Genic enhancers	HUES6 Cell Line	embryonic stem cell
44	chr15:57825000-57827800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr15:57825000-57835800	Weak transcription	HUES64 Cell Line	embryonic stem cell
46	chr15:57825200-57826000	Weak transcription	Fetal Intestine Small	intestine
47	chr15:57825200-57826200	Enhancers	Brain Cingulate Gyrus	brain
48	chr15:57825200-57826200	Enhancers	Right Atrium	heart
49	chr15:57825200-57827400	Enhancers	Left Ventricle	heart
50	chr15:57825400-57826000	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links