Variant report

Variant	rs736902
Chromosome Location	chr9:136929046-136929047
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:136910740..136913816-chr9:136927548..136929923,3	MCF-7	breast:
2	chr9:136928987..136935981-chr9:136998799..137005312,16	MCF-7	breast:
3	chr9:136927905..136930670-chr9:137220083..137221808,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000196363	Chromatin interaction
ENSG00000273249	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10118191	0.82[AMR][1000 genomes]
rs1079524	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10993895	0.90[CHB][hapmap];0.91[JPT][hapmap]
rs1124317	1.00[CEU][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2073818	0.80[CHD][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs2106223	0.91[JPT][hapmap]
rs2157770	0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs2427946	0.88[ASN][1000 genomes]
rs2427949	0.89[ASN][1000 genomes]
rs2427950	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2427951	0.89[ASN][1000 genomes]
rs2427977	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2506696	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2506699	0.88[ASN][1000 genomes]
rs2506700	0.88[ASN][1000 genomes]
rs2506703	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2506712	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2506713	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2506714	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2519078	1.00[CEU][hapmap];0.91[JPT][hapmap];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2519080	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2519081	0.91[CEU][hapmap];0.91[JPT][hapmap];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2520094	0.80[CHD][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs2520095	0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs2520096	0.82[ASN][1000 genomes]
rs2520099	0.82[ASN][1000 genomes]
rs2810489	0.85[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2810491	0.80[CHD][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs2905064	0.82[ASN][1000 genomes]
rs3004622	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3004624	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3004626	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs408307	0.90[CHB][hapmap];0.83[CHD][hapmap];0.91[JPT][hapmap]
rs410876	0.90[CHB][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap]
rs416390	0.90[CHB][hapmap];0.82[CHD][hapmap];0.91[JPT][hapmap]
rs433402	0.90[CHB][hapmap];0.91[JPT][hapmap]
rs443876	0.85[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.94[TSI][hapmap];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs455381	0.90[CHB][hapmap];0.91[JPT][hapmap]
rs457420	0.88[CHD][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs459571	0.91[JPT][hapmap]
rs460154	0.85[CHD][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs464024	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs464826	0.85[ASW][hapmap];0.96[CEU][hapmap];0.87[CHD][hapmap];0.86[JPT][hapmap];0.92[TSI][hapmap];0.89[EUR][1000 genomes]
rs465535	0.91[JPT][hapmap]
rs465724	0.80[CHD][hapmap];0.91[JPT][hapmap]
rs756679	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];0.94[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:29 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv894125	chr9:136723520-136931957	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv831748	chr9:136788484-136944326	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv894132	chr9:136813341-136950691	Active TSS Genic enhancers Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	nsv428226	chr9:136825035-136994606	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv894136	chr9:136839840-136938961	Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
6	nsv894137	chr9:136839840-136950691	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
7	nsv894138	chr9:136839840-137093168	Strong transcription Genic enhancers Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
8	nsv825148	chr9:136848471-137025632	Flanking Bivalent TSS/Enh Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
9	nsv894139	chr9:136863932-136950691	Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Weak transcription ZNF genes & repeats Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
10	nsv894141	chr9:136865879-136938961	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
11	nsv466627	chr9:136870787-136938961	Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
12	nsv615774	chr9:136870787-136938961	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
13	nsv1048571	chr9:136872166-137265444	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
14	nsv894146	chr9:136874066-136938961	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
15	nsv894147	chr9:136874066-136950691	Enhancers Genic enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
16	nsv894148	chr9:136874066-137093168	Enhancers Strong transcription Weak transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
17	nsv894149	chr9:136874158-136950691	Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
18	nsv894150	chr9:136887757-136944827	ZNF genes & repeats Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
19	nsv894151	chr9:136887757-137397609	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers 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 miRNA target site	57 gene(s)	inside rSNPs	diseases
20	nsv466629	chr9:136893867-136938961	Genic enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
21	nsv615779	chr9:136893867-136938961	Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
22	esv1806029	chr9:136906752-136933825	Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
23	nsv430110	chr9:136909280-136964450	Weak transcription Genic enhancers Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
24	nsv894152	chr9:136921015-136950691	Enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Flanking Active TSS Genic enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
25	nsv466630	chr9:136925451-136991034	Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
26	nsv615780	chr9:136925451-136991034	Active TSS Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
27	esv1820789	chr9:136927657-136933825	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
28	esv1832063	chr9:136927657-136933825	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
29	esv1838849	chr9:136927657-136933825	Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs736902	GTF3C4	cis	parietal	SCAN
rs736902	BRD3	cis	multi-tissue	Pritchard

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:136917000-136930800	Weak transcription	K562	blood
2	chr9:136918200-136930800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr9:136918600-136930600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr9:136918800-136930000	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr9:136918800-136930800	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr9:136919200-136930800	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr9:136919400-136930600	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr9:136919800-136930800	Enhancers	Primary T cells fromperipheralblood	blood
9	chr9:136920000-136930800	Enhancers	Ovary	ovary
10	chr9:136920400-136929200	Genic enhancers	Fetal Intestine Small	intestine
11	chr9:136920400-136930800	Enhancers	Fetal Brain Male	brain
12	chr9:136920400-136930800	Enhancers	Left Ventricle	heart
13	chr9:136920600-136930800	Enhancers	Placenta	Placenta
14	chr9:136921800-136930600	Weak transcription	NHLF	lung
15	chr9:136922000-136930400	Weak transcription	NHDF-Ad	bronchial
16	chr9:136922400-136930800	Weak transcription	A549	lung
17	chr9:136922600-136929400	Enhancers	Adipose Nuclei	Adipose
18	chr9:136923400-136930000	Genic enhancers	Brain Germinal Matrix	brain
19	chr9:136923400-136930600	Enhancers	Primary T helper cells PMA-I stimulated	--
20	chr9:136923800-136930600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr9:136923800-136930800	Enhancers	Liver	Liver
22	chr9:136924200-136930800	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr9:136924200-136930800	Enhancers	Primary T helper cells fromperipheralblood	blood
24	chr9:136924600-136930200	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr9:136924600-136930800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr9:136924800-136930400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
27	chr9:136925000-136929400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
28	chr9:136925000-136930400	Weak transcription	Small Intestine	intestine
29	chr9:136925000-136930600	Enhancers	Brain Hippocampus Middle	brain
30	chr9:136925000-136930600	Weak transcription	HUVEC	blood vessel
31	chr9:136925200-136929200	Enhancers	Colonic Mucosa	Colon
32	chr9:136925200-136930600	Enhancers	Primary monocytes fromperipheralblood	blood
33	chr9:136925200-136930600	Weak transcription	NH-A	brain
34	chr9:136925600-136930400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr9:136925600-136930600	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr9:136925800-136929200	Enhancers	Brain Angular Gyrus	brain
37	chr9:136925800-136929400	Enhancers	HSMMtube	muscle
38	chr9:136925800-136930600	Enhancers	Brain Cingulate Gyrus	brain
39	chr9:136925800-136930600	Enhancers	Brain Inferior Temporal Lobe	brain
40	chr9:136926000-136929200	Enhancers	Monocytes-CD14+_RO01746	blood
41	chr9:136926000-136930600	Weak transcription	Primary T cells from cord blood	blood
42	chr9:136926000-136930600	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr9:136926000-136931400	Enhancers	Fetal Heart	heart
44	chr9:136926200-136929200	Enhancers	Stomach Mucosa	stomach
45	chr9:136926200-136930800	Genic enhancers	Fetal Stomach	stomach
46	chr9:136926400-136930000	Weak transcription	Primary neutrophils fromperipheralblood	blood
47	chr9:136926400-136930000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr9:136926400-136930600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr9:136926400-136930600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr9:136926600-136929200	Weak transcription	NHEK	skin

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