Variant report

Variant	rs2746036
Chromosome Location	chr11:32912657-32912658
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:12)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:12 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:32912519-32914604	MCF10A-Er-Src	breast:	n/a	n/a
2	HCFC1	chr11:32912020-32914649	Hela-S3	cervix:	n/a	n/a
3	SP1	chr11:32912637-32913279	H1-hESC	embryonic stem cell:	n/a	n/a
4	STAT3	chr11:32912596-32912772	MCF10A-Er-Src	breast:	n/a	n/a
5	POLR2A	chr11:32912621-32916106	Hela-S3	cervix:	n/a	n/a
6	SP1	chr11:32912656-32913268	H1-hESC	embryonic stem cell:	n/a	n/a
7	KAP1	chr11:32912410-32914048	HEK293	kidney:	n/a	n/a
8	POLR2A	chr11:32912544-32914444	K562	blood:	n/a	n/a
9	JUND	chr11:32912518-32913151	H1-hESC	embryonic stem cell:	n/a	chr11:32912983-32912992
10	POLR2A	chr11:32912403-32913035	SK-N-MC	brain:	n/a	n/a
11	TCF7L2	chr11:32912385-32913982	HEK293	kidney:	n/a	n/a
12	KAP1	chr11:32912454-32913765	U2OS	brain:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:32900766..32903313-chr11:32912451..32914688,2	K562	blood:
2	chr11:32912008..32915658-chr11:33059663..33062231,5	K562	blood:
3	chr11:32911083..32916400-chr11:33180278..33184105,5	K562	blood:
4	chr11:32912444..32914191-chr11:32997049..32998828,2	K562	blood:
5	chr11:32849868..32852880-chr11:32911360..32916794,6	MCF-7	breast:

No data

Variant related genes	Relation type
QSER1	TF binding region
ENSG00000176102	Chromatin interaction
ENSG00000135378	Chromatin interaction
ENSG00000176148	Chromatin interaction
ENSG00000247151	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10454479	1.00[ASW][hapmap];0.86[GIH][hapmap];1.00[MKK][hapmap];1.00[AFR][1000 genomes]
rs10767973	0.94[CEU][hapmap];0.93[GIH][hapmap];0.82[MEX][hapmap];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10767977	1.00[ASN][1000 genomes]
rs10835991	1.00[ASN][1000 genomes]
rs10835996	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10835997	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11032026	1.00[AFR][1000 genomes]
rs11032058	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11032060	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11032071	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11032072	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11032073	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11032074	0.82[MEX][hapmap];1.00[ASN][1000 genomes]
rs11032076	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12224002	1.00[ASN][1000 genomes]
rs2092657	1.00[ASN][1000 genomes]
rs2143572	1.00[AFR][1000 genomes]
rs2249555	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2419772	1.00[ASW][hapmap];1.00[AFR][1000 genomes]
rs2419783	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2746037	0.82[MEX][hapmap];1.00[ASN][1000 genomes]
rs2786800	0.82[MEX][hapmap];1.00[ASN][1000 genomes]
rs35529733	1.00[AFR][1000 genomes]
rs4755476	0.94[CEU][hapmap];1.00[ASN][1000 genomes]
rs4756355	1.00[ASN][1000 genomes]
rs4756373	1.00[ASN][1000 genomes]
rs4756385	1.00[ASN][1000 genomes]
rs589450	1.00[ASN][1000 genomes]
rs602126	1.00[ASN][1000 genomes]
rs6484610	0.82[MEX][hapmap];1.00[ASN][1000 genomes]
rs652963	0.94[CEU][hapmap];0.93[GIH][hapmap];0.82[MEX][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7104368	0.82[MEX][hapmap];1.00[ASN][1000 genomes]
rs7108574	1.00[ASN][1000 genomes]
rs7109890	1.00[ASN][1000 genomes]
rs7113870	1.00[AFR][1000 genomes]
rs7118330	1.00[ASN][1000 genomes]
rs7124151	1.00[AFR][1000 genomes]
rs7128509	1.00[ASN][1000 genomes]
rs73474587	1.00[ASN][1000 genomes]
rs7395190	1.00[ASN][1000 genomes]
rs7481878	0.82[MEX][hapmap];1.00[ASN][1000 genomes]
rs761285	1.00[AFR][1000 genomes]
rs7935374	1.00[AFR][1000 genomes]
rs7941237	1.00[ASN][1000 genomes]
rs7944318	1.00[ASN][1000 genomes]
rs7950261	1.00[AFR][1000 genomes]
rs9919531	1.00[ASN][1000 genomes]
rs9943506	0.88[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758262	chr11:32714643-33049940	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
2	esv2759815	chr11:32714643-33049940	Flanking Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
3	esv2757434	chr11:32792784-32958609	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers 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	36 gene(s)	inside rSNPs	diseases
4	esv34742	chr11:32796092-33004024	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
5	esv2753057	chr11:32796124-33061724	Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
6	esv2753743	chr11:32796124-33084924	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
7	nsv897190	chr11:32801921-32951836	Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2746036	QSER1	cis	cerebellum	SCAN
rs2746036	PRRG4	Cis_1M	lymphoblastoid	RTeQTL
rs2746036	C11orf46	cis	parietal	SCAN
rs2746036	PRRG4	cis	lymphoblastoid	seeQTL

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:32905800-32913400	Weak transcription	Right Atrium	heart
2	chr11:32906800-32913400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr11:32907400-32913000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr11:32908200-32913000	Weak transcription	Liver	Liver
5	chr11:32909200-32912800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr11:32909400-32912800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr11:32909400-32912800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr11:32910000-32912800	Weak transcription	A549	lung
9	chr11:32910000-32913400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr11:32910200-32913800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr11:32910800-32912800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr11:32910800-32913200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr11:32910800-32913400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr11:32910800-32913400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr11:32910800-32913400	Weak transcription	HSMMtube	muscle
16	chr11:32911000-32912800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr11:32911000-32913000	Weak transcription	NH-A	brain
18	chr11:32911000-32913000	Weak transcription	NHDF-Ad	bronchial
19	chr11:32911000-32913000	Weak transcription	NHLF	lung
20	chr11:32911000-32913000	Weak transcription	Osteobl	bone
21	chr11:32911000-32913200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr11:32911000-32913200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr11:32911200-32912800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr11:32911200-32913400	Weak transcription	HSMM	muscle
25	chr11:32912000-32912800	Enhancers	iPS-15b Cell Line	embryonic stem cell
26	chr11:32912000-32912800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
27	chr11:32912000-32913200	Enhancers	Primary hematopoietic stem cells	blood
28	chr11:32912200-32913000	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
29	chr11:32912200-32916400	Active TSS	HUES48 Cell Line	embryonic stem cell
30	chr11:32912400-32912800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr11:32912400-32913000	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
32	chr11:32912400-32913000	Enhancers	Brain Germinal Matrix	brain
33	chr11:32912400-32913000	Enhancers	Fetal Kidney	kidney
34	chr11:32912600-32912800	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
35	chr11:32912600-32912800	Flanking Active TSS	H1 Cell Line	embryonic stem cell
36	chr11:32912600-32912800	Enhancers	Cortex derived primary cultured neurospheres	brain
37	chr11:32912600-32912800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr11:32912600-32912800	Enhancers	Fetal Lung	lung
39	chr11:32912600-32912800	Enhancers	Rectal Mucosa Donor 29	rectum
40	chr11:32912600-32912800	Enhancers	K562	blood
41	chr11:32912600-32913000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr11:32912600-32913000	Enhancers	Fetal Brain Female	brain
43	chr11:32912600-32913000	Enhancers	Hela-S3	cervix
44	chr11:32912600-32913200	Enhancers	Primary hematopoietic stem cells short term culture	blood
45	chr11:32912600-32913400	Enhancers	Fetal Intestine Small	intestine
46	chr11:32912600-32917000	Active TSS	HUES6 Cell Line	embryonic stem cell
47	chr11:32912600-32917000	Active TSS	iPS-20b Cell Line	embryonic stem cell

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