Variant report

Variant	rs17422130
Chromosome Location	chr15:75340457-75340458
allele	C/T
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	chr15:75333297-75341736	GM12878	blood:	n/a	n/a
2	NFATC1	chr15:75339116-75340527	GM12878	blood:	n/a	n/a
3	NFIC	chr15:75338751-75340705	GM12878	blood:	n/a	chr15:75339588-75339604
4	ATF2	chr15:75339118-75340468	GM12878	blood:	n/a	n/a
5	STAT5A	chr15:75338424-75340475	GM12878	blood:	n/a	chr15:75339724-75339732 chr15:75338882-75338893 chr15:75339300-75339312 chr15:75339725-75339737
6	ATF2	chr15:75339021-75340557	GM12878	blood:	n/a	n/a
7	POU2F2	chr15:75339018-75340835	GM12878	blood:	n/a	n/a
8	RUNX3	chr15:75338919-75340485	GM12878	blood:	n/a	n/a
9	MTA3	chr15:75338784-75340743	GM12878	blood:	n/a	n/a
10	POLR2A	chr15:75338482-75340607	GM12878	blood:	n/a	n/a
11	MTA3	chr15:75334888-75340698	GM12878	blood:	n/a	n/a
12	WRNIP1	chr15:75339423-75340492	GM12878	blood:	n/a	n/a
13	POLR2A	chr15:75338392-75340889	GM12892	blood:	n/a	n/a
14	POLR2A	chr15:75333262-75344076	GM12878	blood:	n/a	n/a
15	JUN	chr15:75338798-75340888	K562	blood:	n/a	n/a
16	POLR2A	chr15:75338301-75340525	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:75333855..75341122-chr15:75492635..75495814,9	MCF-7	breast:
2	chr15:75338159..75340815-chr15:75340871..75343132,3	MCF-7	breast:
3	chr15:75334694..75336730-chr15:75338711..75340960,2	MCF-7	breast:
4	chr15:75339319..75341137-chr15:75356875..75359232,2	K562	blood:
5	chr15:75338739..75341398-chr15:75344086..75345973,2	MCF-7	breast:
6	chr15:75334055..75342899-chr15:75492444..75498798,20	K562	blood:
7	chr15:75332512..75342228-chr15:75491817..75496419,22	MCF-7	breast:

Variant related genes	Relation type
PPCDC	TF binding region
ENSG00000138621	Chromatin interaction
ENSG00000167173	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs12050820	0.83[AMR][1000 genomes]
rs12593566	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12900654	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12909515	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1561894	0.86[CHB][hapmap]
rs1867151	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2083730	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2304899	1.00[CEU][hapmap]
rs4627301	0.86[EUR][1000 genomes]
rs4886651	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4886652	0.96[ASN][1000 genomes]
rs6495141	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6495143	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7172565	1.00[CHB][hapmap]
rs9672424	0.84[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv569993	chr15:75242155-75483752	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	72 gene(s)	inside rSNPs	diseases
2	nsv457205	chr15:75336729-75447773	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv569994	chr15:75336729-75447773	Genic enhancers Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75318000-75341400	Weak transcription	Brain Germinal Matrix	brain
2	chr15:75328800-75350400	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr15:75329200-75350400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr15:75329400-75346800	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr15:75333600-75341000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
6	chr15:75334000-75344600	Enhancers	Placenta	Placenta
7	chr15:75334200-75340600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
8	chr15:75334200-75344600	Enhancers	Right Ventricle	heart
9	chr15:75334400-75343200	Enhancers	Fetal Heart	heart
10	chr15:75334600-75340800	Enhancers	Fetal Muscle Leg	muscle
11	chr15:75334600-75341000	Enhancers	Lung	lung
12	chr15:75334600-75343200	Enhancers	Right Atrium	heart
13	chr15:75334800-75344600	Enhancers	Left Ventricle	heart
14	chr15:75335200-75344200	Enhancers	Fetal Lung	lung
15	chr15:75335800-75340600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
16	chr15:75336000-75350400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr15:75336400-75340600	Enhancers	Primary hematopoietic stem cells	blood
18	chr15:75336600-75340600	Enhancers	Small Intestine	intestine
19	chr15:75336600-75343000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr15:75336800-75340600	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr15:75336800-75341200	Enhancers	Primary monocytes fromperipheralblood	blood
22	chr15:75336800-75342400	Enhancers	Brain Cingulate Gyrus	brain
23	chr15:75336800-75342600	Strong transcription	Primary T cells from cord blood	blood
24	chr15:75337200-75353600	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr15:75337400-75340800	Enhancers	Spleen	Spleen
26	chr15:75337600-75340600	Weak transcription	Dnd41	blood
27	chr15:75337600-75341000	Weak transcription	Fetal Brain Female	brain
28	chr15:75337800-75340600	Enhancers	Primary B cells from peripheral blood	blood
29	chr15:75337800-75341000	Enhancers	Fetal Muscle Trunk	muscle
30	chr15:75338000-75341800	Enhancers	Skeletal Muscle Female	skeletal muscle
31	chr15:75338400-75340800	Enhancers	Stomach Mucosa	stomach
32	chr15:75338400-75342000	Genic enhancers	Esophagus	oesophagus
33	chr15:75338400-75342800	Enhancers	Brain Hippocampus Middle	brain
34	chr15:75338600-75340600	Enhancers	Brain Inferior Temporal Lobe	brain
35	chr15:75338600-75340600	Enhancers	HSMMtube	muscle
36	chr15:75338600-75340800	Enhancers	Stomach Smooth Muscle	stomach
37	chr15:75338600-75341000	Enhancers	Sigmoid Colon	Sigmoid Colon
38	chr15:75338600-75342800	Enhancers	Brain Anterior Caudate	brain
39	chr15:75338600-75343200	Enhancers	Pancreas	Pancrea
40	chr15:75338800-75344000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
41	chr15:75339000-75340600	Enhancers	Duodenum Smooth Muscle	Duodenum
42	chr15:75339000-75340800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr15:75339000-75340800	Enhancers	HUVEC	blood vessel
44	chr15:75339000-75342800	Enhancers	Ovary	ovary
45	chr15:75339000-75343000	Enhancers	Brain Angular Gyrus	brain
46	chr15:75339200-75342600	Enhancers	Colon Smooth Muscle	Colon
47	chr15:75339400-75342800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
48	chr15:75339600-75340600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr15:75339600-75340600	Enhancers	Adipose Nuclei	Adipose
50	chr15:75339600-75341600	Weak transcription	Aorta	Aorta

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