Variant report

Variant	rs3814738
Chromosome Location	chr11:66060538-66060539
allele	G/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	MXI1	chr11:66054844-66061017	SK-N-SH	brain:	n/a	chr11:66060557-66060572
2	POLR2A	chr11:66060506-66060538	MCF-7	breast:	n/a	n/a
3	USF1	chr11:66060439-66060732	H1-hESC	embryonic stem cell:	n/a	n/a
4	MAX	chr11:66060366-66060573	NB4	blood:	n/a	n/a
5	POLR2A	chr11:66060371-66060607	MCF-7	breast:	n/a	n/a
6	MAX	chr11:66060262-66060591	K562	blood:	n/a	n/a
7	POLR2A	chr11:66054040-66060816	H1-neurons	neurons:	n/a	n/a
8	MYC	chr11:66060533-66060697	MCF-7	breast:	n/a	n/a
9	BCL3	chr11:66060334-66060683	A549	lung:	n/a	n/a
10	BHLHE40	chr11:66060240-66060618	K562	blood:	n/a	n/a
11	POLR2A	chr11:66059754-66060681	H1-neurons	neurons:	n/a	n/a
12	BHLHE40	chr11:66060189-66060701	HepG2	liver:	n/a	n/a
13	BHLHE40	chr11:66060249-66060579	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:66056831..66061115-chr11:66109718..66114909,6	MCF-7	breast:

Variant related genes	Relation type
YIF1A	TF binding region
ENSG00000174744	Chromatin interaction

Extended variants
information (count: 104 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs10750777	0.83[ASN][1000 genomes]
rs10750778	0.90[ASN][1000 genomes]
rs10750780	0.86[ASN][1000 genomes]
rs10750781	0.97[AFR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10791849	0.81[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs10791850	0.88[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs10791851	0.91[ASN][1000 genomes]
rs10791852	0.91[ASN][1000 genomes]
rs10791854	0.95[ASN][1000 genomes]
rs10791855	0.95[ASN][1000 genomes]
rs10791858	0.97[ASN][1000 genomes]
rs10791859	0.97[ASN][1000 genomes]
rs10791860	0.94[ASN][1000 genomes]
rs10791861	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.96[ASN][1000 genomes]
rs10791862	0.92[ASN][1000 genomes]
rs10791863	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10896080	0.84[ASN][1000 genomes]
rs10896081	0.81[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.93[YRI][hapmap];0.84[ASN][1000 genomes]
rs10896085	0.87[ASN][1000 genomes]
rs10896087	0.87[ASN][1000 genomes]
rs10896089	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10896090	0.91[ASN][1000 genomes]
rs10896091	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.91[ASN][1000 genomes]
rs10896093	0.92[ASN][1000 genomes]
rs10896094	0.92[ASN][1000 genomes]
rs10896098	0.93[ASN][1000 genomes]
rs10896099	0.95[ASN][1000 genomes]
rs10896100	0.94[ASN][1000 genomes]
rs10896105	0.93[ASN][1000 genomes]
rs11227409	0.84[ASN][1000 genomes]
rs11227410	0.81[CEU][hapmap];0.87[YRI][hapmap];0.84[ASN][1000 genomes]
rs11227411	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.84[ASN][1000 genomes]
rs11227413	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.84[ASN][1000 genomes]
rs11227414	0.83[ASN][1000 genomes]
rs11227415	0.81[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.93[YRI][hapmap];0.83[ASN][1000 genomes]
rs11227420	0.91[ASN][1000 genomes]
rs11227433	0.97[ASN][1000 genomes]
rs11227439	0.80[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs11227447	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11227448	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11227452	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11607393	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.84[ASN][1000 genomes]
rs12797158	0.95[ASN][1000 genomes]
rs12797586	0.86[ASN][1000 genomes]
rs12800670	0.95[ASN][1000 genomes]
rs1862005	0.81[ASN][1000 genomes]
rs2017969	0.97[AFR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2155030	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2155031	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2155198	1.00[CEU][hapmap];0.85[YRI][hapmap];0.97[ASN][1000 genomes]
rs2155201	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.97[ASN][1000 genomes]
rs2177053	0.95[ASN][1000 genomes]
rs2177054	0.84[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs2236651	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.97[ASN][1000 genomes]
rs2236652	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.88[MEX][hapmap];0.89[MKK][hapmap];0.93[YRI][hapmap];0.97[ASN][1000 genomes]
rs2276036	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];0.95[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2282568	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2293121	0.84[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.93[YRI][hapmap];0.94[ASN][1000 genomes]
rs2298466	1.00[CHB][hapmap];0.88[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2298468	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2889313	0.87[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs3132851	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3825067	0.81[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.93[YRI][hapmap];0.84[ASN][1000 genomes]
rs3862386	0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs3953856	0.88[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs4013917	0.87[ASN][1000 genomes]
rs4393319	0.97[ASN][1000 genomes]
rs4483592	0.97[ASN][1000 genomes]
rs476551	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs512421	0.94[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs535395	0.81[CEU][hapmap]
rs560393	0.91[ASN][1000 genomes]
rs6591207	0.83[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.93[YRI][hapmap];0.91[ASN][1000 genomes]
rs6591208	0.84[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.93[YRI][hapmap];0.91[ASN][1000 genomes]
rs7124165	1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs7925123	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.97[ASN][1000 genomes]
rs7926402	0.84[ASN][1000 genomes]
rs7929909	0.91[ASN][1000 genomes]
rs7931477	0.87[ASN][1000 genomes]
rs7931544	0.87[ASN][1000 genomes]
rs7935336	0.84[ASN][1000 genomes]
rs7941431	0.93[ASN][1000 genomes]
rs7941469	0.81[CEU][hapmap]
rs7943911	0.91[ASN][1000 genomes]
rs7945723	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7946917	0.89[CHB][hapmap];0.86[CHD][hapmap];0.82[JPT][hapmap];0.93[YRI][hapmap];0.92[ASN][1000 genomes]
rs7951079	0.84[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs918299	0.87[ASN][1000 genomes]
rs9645684	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.86[ASN][1000 genomes]
rs9736673	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3335923	chr11:65741698-66175759	Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
2	esv3407551	chr11:65794503-66158322	Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
3	esv3392427	chr11:65981489-66273695	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	118 gene(s)	inside rSNPs	diseases
4	nsv897771	chr11:66011280-66362997	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	124 gene(s)	inside rSNPs	diseases
5	nsv897772	chr11:66018155-66254085	Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	118 gene(s)	inside rSNPs	diseases
6	nsv897773	chr11:66041807-66063654	Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
7	nsv555223	chr11:66041807-66064126	Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
8	nsv897774	chr11:66042962-66063654	Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
9	nsv897775	chr11:66042962-66064850	Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Strong transcription Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
10	nsv897776	chr11:66042962-66066349	Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
11	nsv897777	chr11:66044882-66063654	Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
12	nsv897778	chr11:66044882-66066349	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
13	nsv897779	chr11:66047523-66063654	Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	34 gene(s)	inside rSNPs	diseases
14	esv3407698	chr11:66058401-66060949	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3814738	PACS1	cis	inferior olivary nucleus	BrainEAC
rs3814738	BAD	cis	parietal	SCAN
rs3814738	PACS1	cis	brain	BrainEAC

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:66056000-66061800	Active TSS	Brain Angular Gyrus	brain
2	chr11:66058400-66060600	Weak transcription	Hela-S3	cervix
3	chr11:66058600-66060800	Bivalent/Poised TSS	Fetal Brain Female	brain
4	chr11:66058800-66060600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
5	chr11:66058800-66060600	Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr11:66059600-66060600	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr11:66059600-66060600	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr11:66059600-66060600	Bivalent Enhancer	Stomach Mucosa	stomach
9	chr11:66059800-66060600	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr11:66059800-66060600	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
11	chr11:66059800-66060600	Bivalent Enhancer	Stomach Smooth Muscle	stomach
12	chr11:66059800-66060800	Bivalent Enhancer	Duodenum Mucosa	Duodenum
13	chr11:66059800-66060800	Bivalent Enhancer	Esophagus	oesophagus
14	chr11:66059800-66066400	Weak transcription	Right Atrium	heart
15	chr11:66060000-66060600	Bivalent/Poised TSS	Brain Germinal Matrix	brain
16	chr11:66060000-66060600	Enhancers	Pancreas	Pancrea
17	chr11:66060000-66064600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr11:66060200-66060600	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
19	chr11:66060200-66060600	Bivalent/Poised TSS	Brain Substantia Nigra	brain
20	chr11:66060200-66061400	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr11:66060400-66060600	Flanking Bivalent TSS/Enh	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr11:66060400-66060600	Flanking Bivalent TSS/Enh	Brain Anterior Caudate	brain
23	chr11:66060400-66060600	Active TSS	Brain Hippocampus Middle	brain
24	chr11:66060400-66060600	Flanking Bivalent TSS/Enh	Brain Inferior Temporal Lobe	brain
25	chr11:66060400-66060600	Bivalent Enhancer	Rectal Mucosa Donor 31	rectum
26	chr11:66060400-66060600	Enhancers	A549	lung
27	chr11:66060400-66060600	Bivalent Enhancer	HepG2	liver
28	chr11:66060400-66060800	Bivalent Enhancer	Fetal Brain Male	brain
29	chr11:66060400-66061000	Enhancers	Gastric	stomach
30	chr11:66060400-66061800	Transcr. at gene 5' and 3'	Brain Cingulate Gyrus	brain
31	chr11:66060400-66063400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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