Variant report

Variant	rs3758947
Chromosome Location	chr11:17501210-17501211
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	SP1	chr11:17501017-17501489	A549	lung:	n/a	chr11:17501298-17501308 chr11:17501298-17501308 chr11:17501326-17501333
2	SP1	chr11:17501030-17501599	H1-hESC	embryonic stem cell:	n/a	chr11:17501298-17501308 chr11:17501298-17501308 chr11:17501326-17501333
3	GTF2F1	chr11:17501066-17501369	H1-hESC	embryonic stem cell:	n/a	n/a
4	ELF1	chr11:17501065-17501352	K562	blood:	n/a	chr11:17501259-17501270
5	YY1	chr11:17501079-17501514	H1-hESC	embryonic stem cell:	n/a	n/a
6	MAZ	chr11:17501192-17501295	HepG2	liver:	n/a	n/a
7	TEAD4	chr11:17501007-17501453	H1-hESC	embryonic stem cell:	n/a	n/a
8	SP1	chr11:17501011-17501434	HepG2	liver:	n/a	chr11:17501298-17501308 chr11:17501298-17501308 chr11:17501326-17501333
9	MAZ	chr11:17501185-17501413	K562	blood:	n/a	n/a
10	JUND	chr11:17501163-17501437	A549	lung:	n/a	n/a
11	KAP1	chr11:17500990-17501600	U2OS	brain:	n/a	n/a
12	SP4	chr11:17500986-17501545	H1-hESC	embryonic stem cell:	n/a	chr11:17501295-17501311
13	STAT3	chr11:17501184-17501323	MCF10A-Er-Src	breast:	n/a	chr11:17501256-17501276
14	ELF1	chr11:17500997-17501476	MCF-7	breast:	n/a	chr11:17501259-17501270
15	RCOR1	chr11:17501135-17501380	K562	blood:	n/a	n/a
16	ATF2	chr11:17500985-17501478	H1-hESC	embryonic stem cell:	n/a	n/a
17	JUND	chr11:17501086-17501768	H1-hESC	embryonic stem cell:	n/a	chr11:17501599-17501608
18	SP1	chr11:17500872-17501807	HCT-116	colon:	n/a	chr11:17501298-17501308 chr11:17501298-17501308 chr11:17501326-17501333
19	JUND	chr11:17501149-17501453	A549	lung:	n/a	n/a
20	YY1	chr11:17501089-17501388	SK-N-SH_RA	brain:	n/a	n/a
21	CREB1	chr11:17501081-17501454	A549	lung:	n/a	n/a
22	SP1	chr11:17500917-17501545	A549	lung:	n/a	chr11:17501298-17501308 chr11:17501298-17501308 chr11:17501326-17501333
23	JUND	chr11:17501095-17501378	H1-hESC	embryonic stem cell:	n/a	n/a
24	YY1	chr11:17501039-17501407	H1-hESC	embryonic stem cell:	n/a	n/a
25	SIN3A	chr11:17501039-17501472	H1-hESC	embryonic stem cell:	n/a	n/a
26	RAD21	chr11:17501065-17501341	SK-N-SH_RA	brain:	n/a	n/a
27	SP4	chr11:17501096-17501457	H1-hESC	embryonic stem cell:	n/a	chr11:17501295-17501311
28	YY1	chr11:17501063-17501375	SK-N-SH_RA	brain:	n/a	n/a
29	KAP1	chr11:17500701-17501650	HEK293	kidney:	n/a	n/a
30	YY1	chr11:17501146-17501396	HCT-116	colon:	n/a	n/a
31	SP1	chr11:17500891-17501661	H1-hESC	embryonic stem cell:	n/a	chr11:17501298-17501308 chr11:17501298-17501308 chr11:17501326-17501333
32	RFX5	chr11:17501078-17501417	H1-hESC	embryonic stem cell:	n/a	n/a
33	JUND	chr11:17501086-17501427	H1-hESC	embryonic stem cell:	n/a	n/a
34	ATF2	chr11:17501035-17501466	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:17494629..17496394-chr11:17499346..17501240,2	MCF-7	breast:
2	chr11:17499490..17502461-chr11:17527268..17529480,2	MCF-7	breast:
3	chr11:17408350..17411098-chr11:17499299..17501931,2	MCF-7	breast:
4	chr11:17497229..17500378-chr11:17500766..17504447,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-OTOG-1	chr11:17498779-17503911	NONHSAT018236

Variant related genes	Relation type
ABCC8	TF binding region
ENSG00000006071	Chromatin interaction
ENSG00000187486	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10832793	0.83[ASN][1000 genomes]
rs11603988	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];0.88[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11823850	1.00[CEU][hapmap];0.85[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2072229	1.00[CEU][hapmap];0.82[JPT][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2270023	0.89[CEU][hapmap];0.85[AMR][1000 genomes]
rs3758948	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66902740	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469895	chr11:17368270-17584220	Weak transcription Bivalent Enhancer Genic enhancers Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3758947	LDHAL6A	cis	cerebellum	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:17498800-17502000	Enhancers	Dnd41	blood
2	chr11:17500400-17501400	Flanking Active TSS	Brain Substantia Nigra	brain
3	chr11:17500600-17501600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr11:17500600-17501600	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr11:17500600-17501800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr11:17500600-17502000	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
7	chr11:17500800-17502000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
8	chr11:17501000-17501400	Active TSS	Brain Angular Gyrus	brain
9	chr11:17501000-17501400	Active TSS	Brain Anterior Caudate	brain
10	chr11:17501000-17501400	Active TSS	Brain Cingulate Gyrus	brain
11	chr11:17501000-17501400	Active TSS	Brain Hippocampus Middle	brain
12	chr11:17501000-17501400	Active TSS	Brain Inferior Temporal Lobe	brain
13	chr11:17501000-17501400	Active TSS	Fetal Brain Male	brain
14	chr11:17501000-17501400	Active TSS	Fetal Brain Female	brain
15	chr11:17501000-17501600	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
16	chr11:17501000-17501600	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
17	chr11:17501000-17501600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
18	chr11:17501000-17501600	Enhancers	Gastric	stomach
19	chr11:17501000-17501600	Enhancers	Left Ventricle	heart
20	chr11:17501000-17501600	Enhancers	Pancreas	Pancrea
21	chr11:17501200-17501400	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
22	chr11:17501200-17501400	Active TSS	HUES64 Cell Line	embryonic stem cell
23	chr11:17501200-17501400	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
24	chr11:17501200-17501400	Active TSS	iPS-18 Cell Line	embryonic stem cell
25	chr11:17501200-17501400	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
26	chr11:17501200-17501400	Enhancers	Cortex derived primary cultured neurospheres	brain
27	chr11:17501200-17501400	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr11:17501200-17501400	Enhancers	Colon Smooth Muscle	Colon
29	chr11:17501200-17501400	Bivalent Enhancer	Fetal Stomach	stomach
30	chr11:17501200-17501600	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr11:17501200-17501600	Bivalent/Poised TSS	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr11:17501200-17501600	Enhancers	Brain Germinal Matrix	brain
33	chr11:17501200-17501600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
34	chr11:17501200-17501600	Enhancers	Fetal Intestine Large	intestine
35	chr11:17501200-17501600	Enhancers	Fetal Intestine Small	intestine
36	chr11:17501200-17501800	Enhancers	H9 Cell Line	embryonic stem cell
37	chr11:17501200-17502000	Enhancers	HUES48 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links