Variant report

Variant	rs2306780
Chromosome Location	chr15:59515446-59515447
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	chr15:59514999-59516437	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr15:59514852-59516662	A549	lung:	n/a	n/a
3	POLR2A	chr15:59514913-59515791	GM12892	blood:	n/a	n/a
4	POLR2A	chr15:59515442-59515783	GM12878	blood:	n/a	n/a
5	POLR2A	chr15:59515406-59515859	GM12891	blood:	n/a	n/a
6	USF2	chr15:59515003-59515743	Hela-S3	cervix:	n/a	chr15:59515555-59515566
7	GATA2	chr15:59515191-59515507	SH-SY5Y	brain:	n/a	n/a
8	POLR2A	chr15:59514902-59517880	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr15:59514936-59515887	GM12891	blood:	n/a	n/a
10	POLR2A	chr15:59514933-59515884	GM12878	blood:	n/a	n/a
11	NR3C1	chr15:59515354-59515867	A549	lung:	n/a	n/a
12	POLR2A	chr15:59514869-59517290	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:59509480..59512109-chr15:59514954..59517211,4	K562	blood:

Variant related genes	Relation type
MYO1E	TF binding region
ENSG00000157483	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11634548	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11638386	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12438740	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2230155	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2306779	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35481817	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3794491	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3794492	1.00[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3794493	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3816813	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4775131	0.96[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4775135	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7167638	0.90[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73422960	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv527307	chr15:59103328-60018487	Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	145 gene(s)	inside rSNPs	diseases
2	nsv833025	chr15:59336148-59522176	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv1035868	chr15:59402426-59530594	Flanking Active TSS Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv833027	chr15:59474806-59608544	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv904272	chr15:59500577-59549018	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	nsv977071	chr15:59509537-59519089	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:59467800-59523200	Weak transcription	Fetal Brain Female	brain
2	chr15:59468200-59528600	Weak transcription	Stomach Mucosa	stomach
3	chr15:59468600-59521400	Strong transcription	Rectal Mucosa Donor 29	rectum
4	chr15:59475800-59517800	Strong transcription	HUES48 Cell Line	embryonic stem cell
5	chr15:59485600-59521200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr15:59487800-59524400	Weak transcription	Small Intestine	intestine
7	chr15:59489800-59515600	Weak transcription	Right Atrium	heart
8	chr15:59492000-59521600	Strong transcription	Rectal Mucosa Donor 31	rectum
9	chr15:59493200-59523200	Strong transcription	Hela-S3	cervix
10	chr15:59496800-59515600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
11	chr15:59496800-59522000	Strong transcription	NHEK	skin
12	chr15:59497000-59524800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr15:59497200-59517600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr15:59498000-59516000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr15:59498800-59522000	Strong transcription	GM12878-XiMat	blood
16	chr15:59500000-59517600	Weak transcription	Fetal Lung	lung
17	chr15:59500000-59524400	Weak transcription	Right Ventricle	heart
18	chr15:59500600-59524600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr15:59501200-59521400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr15:59501200-59523400	Weak transcription	Ovary	ovary
21	chr15:59501200-59525600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr15:59502800-59525800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr15:59503800-59518000	Strong transcription	Sigmoid Colon	Sigmoid Colon
24	chr15:59504000-59520200	Strong transcription	Liver	Liver
25	chr15:59504800-59517800	Strong transcription	Primary monocytes fromperipheralblood	blood
26	chr15:59505200-59516000	Weak transcription	Brain Anterior Caudate	brain
27	chr15:59505800-59518000	Strong transcription	HUES64 Cell Line	embryonic stem cell
28	chr15:59506800-59517400	Strong transcription	H1 Cell Line	embryonic stem cell
29	chr15:59509600-59516200	Weak transcription	Psoas Muscle	Psoas
30	chr15:59510200-59516200	Weak transcription	Esophagus	oesophagus
31	chr15:59510200-59516600	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr15:59511200-59515600	Strong transcription	Adipose Nuclei	Adipose
33	chr15:59511400-59515600	Weak transcription	Brain Cingulate Gyrus	brain
34	chr15:59511400-59549200	Weak transcription	Colonic Mucosa	Colon
35	chr15:59511600-59517400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr15:59511800-59517200	Strong transcription	Primary B cells from cord blood	blood
37	chr15:59512200-59521600	Strong transcription	Fetal Intestine Small	intestine
38	chr15:59512400-59515600	Weak transcription	Aorta	Aorta
39	chr15:59512400-59518400	Strong transcription	Duodenum Mucosa	Duodenum
40	chr15:59512600-59520000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr15:59513400-59515800	Genic enhancers	NH-A	brain
42	chr15:59513400-59516400	Genic enhancers	HUVEC	blood vessel
43	chr15:59513400-59516600	Genic enhancers	NHDF-Ad	bronchial
44	chr15:59513400-59517600	Strong transcription	HUES6 Cell Line	embryonic stem cell
45	chr15:59513400-59517800	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr15:59513400-59520200	Strong transcription	Primary B cells from peripheral blood	blood
47	chr15:59513400-59521600	Strong transcription	Fetal Intestine Large	intestine
48	chr15:59513600-59516000	Enhancers	Brain Substantia Nigra	brain
49	chr15:59513600-59516400	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr15:59513600-59516400	Enhancers	Fetal Kidney	kidney

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