Variant report

Variant	rs11795331
Chromosome Location	chr9:97040815-97040816
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	ARID3A	chr9:97040732-97041408	K562	blood:	n/a	n/a
2	TBL1XR1	chr9:97040561-97041424	K562	blood:	n/a	n/a
3	GATA3	chr9:97040717-97041546	MCF-7	breast:	n/a	chr9:97041245-97041252 chr9:97041241-97041257 chr9:97041245-97041252 chr9:97041245-97041252
4	ELF1	chr9:97040460-97040838	HepG2	liver:	n/a	chr9:97040645-97040658
5	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
6	MAX	chr9:97040752-97041507	A549	lung:	n/a	chr9:97041237-97041246 chr9:97041285-97041294
7	TCF12	chr9:97040619-97041502	A549	lung:	n/a	n/a
8	RAD21	chr9:97040740-97041375	Hela-S3	cervix:	n/a	chr9:97040850-97040864
9	GATA3	chr9:97040706-97041526	A549	lung:	n/a	chr9:97041245-97041252 chr9:97041241-97041257 chr9:97041245-97041252 chr9:97041245-97041252
10	RCOR1	chr9:97040459-97041487	K562	blood:	n/a	n/a
11	HCFC1	chr9:97040655-97041243	K562	blood:	n/a	n/a
12	CEBPB	chr9:97040772-97041428	A549	lung:	n/a	n/a
13	MYC	chr9:97040579-97041448	K562	blood:	n/a	chr9:97041237-97041246 chr9:97041285-97041294
14	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
15	ZNF217	chr9:97040782-97041402	MCF-7	breast:	n/a	n/a
16	MAZ	chr9:97040517-97041412	K562	blood:	n/a	chr9:97041237-97041246 chr9:97041285-97041294
17	FOXA2	chr9:97040488-97041463	A549	lung:	n/a	n/a
18	MAFF	chr9:97040591-97040872	K562	blood:	n/a	n/a
19	GATA1	chr9:97040460-97041588	K562	blood:	n/a	chr9:97041245-97041252 chr9:97041241-97041257 chr9:97041245-97041252 chr9:97041245-97041252
20	TEAD4	chr9:97040355-97041454	K562	blood:	n/a	n/a
21	CTCF	chr9:97040561-97040889	K562	blood:	n/a	n/a
22	ELF1	chr9:97040408-97040818	K562	blood:	n/a	chr9:97040645-97040658
23	SP1	chr9:97040780-97041566	A549	lung:	n/a	n/a
24	MAFK	chr9:97040559-97040833	K562	blood:	n/a	n/a
25	ELF1	chr9:97040396-97041444	MCF-7	breast:	n/a	chr9:97040645-97040658
26	SIN3AK20	chr9:97040694-97041523	MCF-7	breast:	n/a	n/a
27	CUX1	chr9:97040752-97040859	K562	blood:	n/a	n/a
28	FOS	chr9:97040790-97041457	HUVEC	blood vessel:	n/a	chr9:97041375-97041385 chr9:97041285-97041292 chr9:97041237-97041246 chr9:97041235-97041247 chr9:97041285-97041293 chr9:97041375-97041385 chr9:97041285-97041293 chr9:97041283-97041294 chr9:97041235-97041246
29	ELF1	chr9:97040805-97041495	MCF-7	breast:	n/a	n/a
30	FOSL2	chr9:97040726-97041466	A549	lung:	n/a	chr9:97041375-97041385 chr9:97041285-97041292 chr9:97041237-97041246 chr9:97041235-97041247 chr9:97041285-97041293 chr9:97041375-97041385 chr9:97041285-97041293
31	FOXA1	chr9:97040511-97040867	HepG2	liver:	n/a	n/a
32	EP300	chr9:97040360-97041524	K562	blood:	n/a	chr9:97041285-97041294 chr9:97041237-97041246 chr9:97041164-97041178
33	ZNF384	chr9:97040511-97041303	K562	blood:	n/a	n/a
34	POLR2A	chr9:97040811-97041372	K562	blood:	n/a	n/a
35	RFX5	chr9:97040734-97041379	Hela-S3	cervix:	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]
rs11793128	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
rs11795331	HIATL1	cis	lung	GTEx
rs11795331	FLJ14753	cis	multi-tissue	Pritchard
rs11795331	RP11-307E17.8	cis	Esophagus Muscularis	GTEx
rs11795331	HIATL1	cis	lymphoblastoid	seeQTL

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97022200-97041800	Weak transcription	Fetal Lung	lung
2	chr9:97022200-97042600	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr9:97022200-97055200	Weak transcription	Aorta	Aorta
4	chr9:97022600-97055200	Weak transcription	Stomach Smooth Muscle	stomach
5	chr9:97022800-97042400	Weak transcription	Brain Angular Gyrus	brain
6	chr9:97022800-97054600	Weak transcription	Pancreas	Pancrea
7	chr9:97023000-97041000	Weak transcription	Adipose Nuclei	Adipose
8	chr9:97023000-97041000	Weak transcription	Ovary	ovary
9	chr9:97023000-97041800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr9:97023000-97041800	Weak transcription	Esophagus	oesophagus
11	chr9:97023000-97050000	Weak transcription	Right Ventricle	heart
12	chr9:97023000-97055400	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr9:97023400-97042800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr9:97024000-97041200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr9:97029600-97041800	Weak transcription	Spleen	Spleen
16	chr9:97030200-97048400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr9:97030400-97042200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr9:97031800-97041000	Weak transcription	Left Ventricle	heart
19	chr9:97031800-97050400	Weak transcription	Psoas Muscle	Psoas
20	chr9:97032000-97041800	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr9:97032400-97041600	Weak transcription	Fetal Intestine Small	intestine
22	chr9:97032400-97064600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr9:97032600-97041800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr9:97032800-97042200	Weak transcription	Fetal Kidney	kidney
25	chr9:97033600-97041800	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr9:97033600-97054600	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr9:97034000-97041000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr9:97034000-97042400	Weak transcription	HMEC	breast
29	chr9:97034400-97041600	Weak transcription	Rectal Smooth Muscle	rectum
30	chr9:97034800-97041000	Weak transcription	Fetal Thymus	thymus
31	chr9:97035200-97041000	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr9:97035400-97042000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr9:97035600-97042200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr9:97036800-97062600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr9:97037200-97042000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr9:97037400-97050200	Weak transcription	Colon Smooth Muscle	Colon
37	chr9:97037600-97044600	Weak transcription	Fetal Stomach	stomach
38	chr9:97038800-97041600	Strong transcription	Primary B cells from cord blood	blood
39	chr9:97039000-97041000	Weak transcription	Fetal Brain Female	brain
40	chr9:97039200-97041000	Weak transcription	Liver	Liver
41	chr9:97039200-97053600	Weak transcription	Brain Hippocampus Middle	brain
42	chr9:97039200-97055000	Weak transcription	Brain Substantia Nigra	brain
43	chr9:97039200-97062600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr9:97039400-97054600	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr9:97039400-97067600	Weak transcription	Brain Cingulate Gyrus	brain
46	chr9:97039600-97041200	Weak transcription	Brain Anterior Caudate	brain
47	chr9:97039800-97042000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr9:97040000-97064600	Weak transcription	Brain Germinal Matrix	brain
49	chr9:97040200-97041400	Enhancers	HepG2	liver
50	chr9:97040200-97041800	Enhancers	Hela-S3	cervix

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