Variant report

Variant	rs11793128
Chromosome Location	chr9:97040683-97040684
allele	A/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	TBL1XR1	chr9:97040561-97041424	K562	blood:	n/a	n/a
2	ELF1	chr9:97040460-97040838	HepG2	liver:	n/a	chr9:97040645-97040658
3	JUND	chr9:97040307-97041502	K562	blood:	n/a	chr9:97041375-97041385 chr9:97041285-97041292 chr9:97041237-97041246 chr9:97041235-97041247 chr9:97041285-97041293 chr9:97041375-97041385 chr9:97041285-97041293 chr9:97041235-97041246
4	TCF12	chr9:97040619-97041502	A549	lung:	n/a	n/a
5	RCOR1	chr9:97040459-97041487	K562	blood:	n/a	n/a
6	HCFC1	chr9:97040655-97041243	K562	blood:	n/a	n/a
7	MYC	chr9:97040579-97041448	K562	blood:	n/a	chr9:97041237-97041246 chr9:97041285-97041294
8	JUN	chr9:97040311-97041500	K562	blood:	n/a	chr9:97041375-97041385 chr9:97041285-97041292 chr9:97041237-97041246 chr9:97041235-97041247 chr9:97041285-97041293 chr9:97041375-97041385 chr9:97041285-97041293
9	MAZ	chr9:97040517-97041412	K562	blood:	n/a	chr9:97041237-97041246 chr9:97041285-97041294
10	FOXA2	chr9:97040488-97041463	A549	lung:	n/a	n/a
11	MAFF	chr9:97040591-97040872	K562	blood:	n/a	n/a
12	GATA1	chr9:97040460-97041588	K562	blood:	n/a	chr9:97041245-97041252 chr9:97041241-97041257 chr9:97041245-97041252 chr9:97041245-97041252
13	TEAD4	chr9:97040355-97041454	K562	blood:	n/a	n/a
14	CTCF	chr9:97040561-97040889	K562	blood:	n/a	n/a
15	ELF1	chr9:97040408-97040818	K562	blood:	n/a	chr9:97040645-97040658
16	MAFK	chr9:97040559-97040833	K562	blood:	n/a	n/a
17	ELF1	chr9:97040396-97041444	MCF-7	breast:	n/a	chr9:97040645-97040658
18	FOXA1	chr9:97040511-97040867	HepG2	liver:	n/a	n/a
19	EP300	chr9:97040360-97041524	K562	blood:	n/a	chr9:97041285-97041294 chr9:97041237-97041246 chr9:97041164-97041178
20	ZNF384	chr9:97040511-97041303	K562	blood:	n/a	n/a
21	BHLHE40	chr9:97040551-97040706	K562	blood:	n/a	n/a
22	ELF1	chr9:97040502-97040767	HepG2	liver:	n/a	chr9:97040645-97040658
23	FOXA1	chr9:97040512-97040781	HepG2	liver:	n/a	n/a
24	FOXA1	chr9:97040540-97040809	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:97021406..97023043-chr9:97038524..97041223,2	K562	blood:
2	chr9:97021249..97023395-chr9:97039780..97042509,4	MCF-7	breast:
3	chr9:97038732..97040918-chr9:97062017..97064151,2	K562	blood:

Variant related genes	Relation type
ZNF169	TF binding region
ENSG00000175787	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs11789111	0.83[AMR][1000 genomes]
rs11791619	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs11792912	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11795331	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12003203	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12343123	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs1536690	0.85[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1878875	0.82[JPT][hapmap]
rs2094526	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4602957	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4744330	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs56849060	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs58109458	0.81[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs58759607	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59962706	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62578818	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs62578821	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs62578822	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62578823	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6479545	0.82[CHB][hapmap]
rs7019137	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs7025878	0.82[JPT][hapmap]
rs7034153	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs7036474	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs7037298	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs7045712	0.85[CHB][hapmap]
rs7046779	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs722353	0.82[JPT][hapmap]
rs73653456	0.98[ASN][1000 genomes]
rs7854893	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7859571	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs7871267	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7874441	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9299417	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap]
rs9632920	0.85[CHB][hapmap]

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	nsv831655	chr9:96834042-97042009	Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	218 gene(s)	inside rSNPs	diseases
2	esv3394266	chr9:96935210-97045514	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS 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	195 gene(s)	inside rSNPs	diseases
3	nsv893592	chr9:96973995-97295269	Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	nsv1046906	chr9:96999227-97239809	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	esv2761545	chr9:97025298-97356950	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS 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	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11793128	RP11-307E17.8	cis	Esophagus Muscularis	GTEx
rs11793128	FLJ14753	cis	multi-tissue	Pritchard
rs11793128	HIATL1	cis	lymphoblastoid	seeQTL
rs11793128	HIATL1	cis	lung	GTEx

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97022200-97040800	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr9:97022200-97041800	Weak transcription	Fetal Lung	lung
3	chr9:97022200-97042600	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr9:97022200-97055200	Weak transcription	Aorta	Aorta
5	chr9:97022600-97055200	Weak transcription	Stomach Smooth Muscle	stomach
6	chr9:97022800-97040800	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr9:97022800-97040800	Weak transcription	Thymus	Thymus
8	chr9:97022800-97042400	Weak transcription	Brain Angular Gyrus	brain
9	chr9:97022800-97054600	Weak transcription	Pancreas	Pancrea
10	chr9:97023000-97040800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr9:97023000-97040800	Weak transcription	Lung	lung
12	chr9:97023000-97041000	Weak transcription	Adipose Nuclei	Adipose
13	chr9:97023000-97041000	Weak transcription	Ovary	ovary
14	chr9:97023000-97041800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr9:97023000-97041800	Weak transcription	Esophagus	oesophagus
16	chr9:97023000-97050000	Weak transcription	Right Ventricle	heart
17	chr9:97023000-97055400	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr9:97023400-97042800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr9:97023600-97040800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr9:97024000-97041200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr9:97029600-97041800	Weak transcription	Spleen	Spleen
22	chr9:97030200-97048400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr9:97030400-97040800	Weak transcription	Primary T cells fromperipheralblood	blood
24	chr9:97030400-97042200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr9:97031800-97041000	Weak transcription	Left Ventricle	heart
26	chr9:97031800-97050400	Weak transcription	Psoas Muscle	Psoas
27	chr9:97032000-97041800	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr9:97032400-97041600	Weak transcription	Fetal Intestine Small	intestine
29	chr9:97032400-97064600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr9:97032600-97041800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr9:97032800-97042200	Weak transcription	Fetal Kidney	kidney
32	chr9:97033000-97040800	Weak transcription	Dnd41	blood
33	chr9:97033600-97041800	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr9:97033600-97054600	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr9:97034000-97041000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr9:97034000-97042400	Weak transcription	HMEC	breast
37	chr9:97034400-97041600	Weak transcription	Rectal Smooth Muscle	rectum
38	chr9:97034800-97040800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr9:97034800-97041000	Weak transcription	Fetal Thymus	thymus
40	chr9:97035200-97041000	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr9:97035400-97040800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr9:97035400-97042000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
43	chr9:97035600-97042200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr9:97036400-97040800	Weak transcription	Fetal Muscle Leg	muscle
45	chr9:97036600-97040800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr9:97036800-97062600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr9:97037200-97040800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr9:97037200-97042000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr9:97037400-97050200	Weak transcription	Colon Smooth Muscle	Colon
50	chr9:97037600-97040800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links