Variant report

Variant	rs693235
Chromosome Location	chr11:64492762-64492763
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	POLR2A	chr11:64491342-64494192	HL-60	blood:	n/a	n/a
2	CEBPB	chr11:64492541-64492919	HepG2	liver:	n/a	n/a
3	CEBPB	chr11:64492600-64492940	HepG2	liver:	n/a	n/a
4	POLR2A	chr11:64491423-64494233	HL-60	blood:	n/a	n/a
5	MYC	chr11:64492701-64492871	HepG2	liver:	n/a	n/a
6	CEBPD	chr11:64492639-64492834	HepG2	liver:	n/a	n/a
7	POLR2A	chr11:64492744-64493392	H1-neurons	neurons:	n/a	n/a
8	CEBPB	chr11:64492622-64492789	HepG2	liver:	n/a	n/a
9	HNF4G	chr11:64492504-64492907	HepG2	liver:	n/a	chr11:64492840-64492852 chr11:64492705-64492718 chr11:64492839-64492852 chr11:64492706-64492718 chr11:64492706-64492718 chr11:64492835-64492857 chr11:64492705-64492718 chr11:64492701-64492723 chr11:64492839-64492852 chr11:64492705-64492720 chr11:64492636-64492648 chr11:64492841-64492853 chr11:64492705-64492720 chr11:64492703-64492721 chr11:64492707-64492719 chr11:64492704-64492712 chr11:64492840-64492852 chr11:64492705-64492719 chr11:64492840-64492853 chr11:64492839-64492853 chr11:64492703-64492718 chr11:64492706-64492719
10	HDAC2	chr11:64492511-64492891	HepG2	liver:	n/a	n/a
11	MAZ	chr11:64492762-64492783	HepG2	liver:	n/a	n/a
12	SP1	chr11:64492463-64492892	HepG2	liver:	n/a	chr11:64492865-64492874
13	HNF4A	chr11:64492488-64492903	HepG2	liver:	n/a	chr11:64492840-64492852 chr11:64492705-64492718 chr11:64492839-64492852 chr11:64492706-64492718 chr11:64492706-64492718 chr11:64492835-64492857 chr11:64492705-64492718 chr11:64492701-64492723 chr11:64492839-64492852 chr11:64492705-64492720 chr11:64492636-64492648 chr11:64492841-64492853 chr11:64492705-64492720 chr11:64492703-64492721 chr11:64492707-64492719 chr11:64492704-64492712 chr11:64492704-64492719 chr11:64492840-64492852 chr11:64492705-64492719 chr11:64492840-64492853 chr11:64492839-64492853 chr11:64492706-64492719
14	HNF4A	chr11:64492570-64492838	HepG2	liver:	n/a	chr11:64492705-64492718 chr11:64492706-64492718 chr11:64492706-64492718 chr11:64492705-64492718 chr11:64492701-64492723 chr11:64492705-64492720 chr11:64492636-64492648 chr11:64492705-64492720 chr11:64492703-64492721 chr11:64492707-64492719 chr11:64492704-64492712 chr11:64492704-64492719 chr11:64492705-64492719 chr11:64492706-64492719
15	CEBPB	chr11:64492563-64492906	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:64489234..64490973-chr11:64491983..64494707,2	K562	blood:
2	chr11:64485321..64487763-chr11:64492091..64495003,2	K562	blood:
3	chr11:64492501..64495371-chr11:64543790..64546396,3	K562	blood:

Variant related genes	Relation type
NRXN2	TF binding region
ENSG00000110076	Chromatin interaction
ENSG00000168066	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10897524	0.92[GIH][hapmap];0.85[JPT][hapmap];0.87[TSI][hapmap];0.85[AMR][1000 genomes]
rs11231859	0.90[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1143937	0.90[CEU][hapmap]
rs1207181	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs1633462	0.89[CEU][hapmap]
rs17146121	0.80[CEU][hapmap];0.89[GIH][hapmap];0.89[MEX][hapmap];0.87[TSI][hapmap]
rs2003293	0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2073798	0.88[ASW][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes]
rs2230414	0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2267918	0.94[ASW][hapmap];0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2284301	0.90[CEU][hapmap];0.88[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap];0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2375335	0.90[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2959652	0.90[CEU][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.88[AMR][1000 genomes]
rs3741398	0.90[CEU][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap]
rs3809076	0.80[CEU][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.89[MEX][hapmap];0.93[TSI][hapmap]
rs474707	0.91[CEU][hapmap];0.89[MEX][hapmap];0.94[TSI][hapmap]
rs476037	0.80[CEU][hapmap];0.82[CHD][hapmap];0.89[GIH][hapmap];0.89[MEX][hapmap]
rs477549	0.90[CEU][hapmap];0.89[MEX][hapmap];0.88[TSI][hapmap]
rs483962	0.90[CEU][hapmap];0.89[MEX][hapmap];0.94[TSI][hapmap]
rs487105	0.90[CEU][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap]
rs489192	0.90[CEU][hapmap];0.80[JPT][hapmap];0.89[MEX][hapmap]
rs494128	0.83[AMR][1000 genomes]
rs496914	0.88[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.96[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs523200	0.90[CEU][hapmap];0.94[MEX][hapmap];0.88[TSI][hapmap]
rs532747	0.92[GIH][hapmap];0.89[MEX][hapmap];0.86[TSI][hapmap]
rs547066	0.84[GIH][hapmap];0.88[MEX][hapmap];0.86[TSI][hapmap]
rs555974	0.81[AMR][1000 genomes]
rs569602	0.92[GIH][hapmap];0.90[JPT][hapmap];0.89[MEX][hapmap];0.86[TSI][hapmap]
rs580374	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs58483071	0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs589691	0.90[CEU][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap]
rs606458	0.90[CEU][hapmap];0.94[MEX][hapmap];0.88[TSI][hapmap]
rs607389	0.90[CEU][hapmap]
rs624975	0.81[CEU][hapmap]
rs625172	0.81[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.80[AMR][1000 genomes]
rs637332	0.90[CEU][hapmap];0.89[MEX][hapmap];0.94[TSI][hapmap]
rs667237	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes]
rs669976	0.81[CEU][hapmap]
rs677298	0.90[CEU][hapmap]
rs680273	0.90[CEU][hapmap];0.94[MEX][hapmap];0.88[TSI][hapmap]
rs7939965	0.80[CEU][hapmap];0.80[CHD][hapmap];0.89[GIH][hapmap];0.89[MEX][hapmap];0.87[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv468596	chr11:64334114-64527080	Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv555195	chr11:64334114-64527080	Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv897694	chr11:64334114-64584959	Weak transcription Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
4	nsv818842	chr11:64345448-64546391	Bivalent Enhancer Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
5	nsv528506	chr11:64345448-64701030	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1075 gene(s)	inside rSNPs	diseases
6	nsv555196	chr11:64357072-64559898	Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
7	nsv897695	chr11:64357072-64701030	Weak transcription Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1075 gene(s)	inside rSNPs	diseases
8	nsv1051350	chr11:64372906-64533632	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
9	nsv555198	chr11:64373899-64573589	Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
10	esv1804443	chr11:64386453-64534785	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
11	nsv897697	chr11:64447420-64584959	Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
12	nsv897698	chr11:64447420-64621573	Active TSS Bivalent Enhancer Genic enhancers Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
13	nsv897699	chr11:64447420-64638041	Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
14	nsv897700	chr11:64447420-64701030	Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1071 gene(s)	inside rSNPs	diseases
15	nsv359	chr11:64477008-64502873	Bivalent/Poised TSS Flanking Active TSS Genic enhancers Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
16	nsv555202	chr11:64477050-64573589	Strong transcription Bivalent/Poised TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
17	nsv468597	chr11:64477050-64584959	Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
18	nsv468598	chr11:64477050-64584959	Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
19	nsv555203	chr11:64477050-64584959	Strong transcription Genic enhancers Bivalent Enhancer Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
20	nsv1049744	chr11:64486615-64630149	Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
21	nsv832189	chr11:64487183-64620199	Weak transcription Transcr. at gene 5' and 3' Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs693235	SF1	cis	lymphoblastoid	seeQTL
rs693235	SF1	Cis_1M	lymphoblastoid	RTeQTL
rs693235	CABP2	cis	parietal	SCAN
rs693235	PYGM	cis	cerebellum	SCAN
rs693235	PYGM	cis	parietal	SCAN
rs693235	ANKRD13D	cis	parietal	SCAN
rs693235	TMEM138	cis	parietal	SCAN
rs693235	EHD1	cis	cerebellum	SCAN
rs693235	B3GNT1	cis	cerebellum	SCAN
rs693235	SF1	cis	multi-tissue	Pritchard
rs693235	RASGRP2	cis	parietal	SCAN
rs693235	MALAT1	cis	parietal	SCAN
rs693235	TMEM138	cis	cerebellum	SCAN
rs693235	POLA2	cis	cerebellum	SCAN

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:64490800-64498000	Enhancers	Liver	Liver
2	chr11:64491000-64494200	Enhancers	Fetal Brain Male	brain
3	chr11:64491000-64502200	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr11:64491200-64492800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr11:64491200-64492800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
6	chr11:64491200-64493000	Enhancers	Primary hematopoietic stem cells	blood
7	chr11:64491200-64493000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
8	chr11:64491200-64493200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr11:64491200-64493600	Enhancers	Primary hematopoietic stem cells short term culture	blood
10	chr11:64491200-64493600	Enhancers	Fetal Thymus	thymus
11	chr11:64491200-64493800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr11:64491200-64494000	Enhancers	Primary T cells fromperipheralblood	blood
13	chr11:64491200-64494200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr11:64491200-64494200	Enhancers	HUES6 Cell Line	embryonic stem cell
15	chr11:64491200-64494200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
16	chr11:64491200-64494400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr11:64491200-64494800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr11:64491200-64496000	Weak transcription	Aorta	Aorta
19	chr11:64491200-64496200	Weak transcription	Lung	lung
20	chr11:64491200-64497600	Weak transcription	Right Ventricle	heart
21	chr11:64491200-64499200	Weak transcription	Left Ventricle	heart
22	chr11:64491200-64502200	Weak transcription	Rectal Smooth Muscle	rectum
23	chr11:64491200-64502400	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr11:64491200-64502800	Weak transcription	Gastric	stomach
25	chr11:64491400-64493000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
26	chr11:64491400-64493200	Enhancers	Primary B cells from peripheral blood	blood
27	chr11:64491400-64493200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr11:64491400-64493400	Enhancers	Primary B cells from cord blood	blood
29	chr11:64491400-64493600	Enhancers	Monocytes-CD14+_RO01746	blood
30	chr11:64491400-64493800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr11:64491400-64494200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr11:64491400-64494400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr11:64491400-64494600	Enhancers	H1 Cell Line	embryonic stem cell
34	chr11:64491400-64494800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
35	chr11:64491400-64494800	Enhancers	Cortex derived primary cultured neurospheres	brain
36	chr11:64491400-64502200	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr11:64491400-64503000	Weak transcription	Colon Smooth Muscle	Colon
38	chr11:64491400-64509400	Weak transcription	Right Atrium	heart
39	chr11:64491400-64509600	Weak transcription	Brain Angular Gyrus	brain
40	chr11:64491400-64509600	Weak transcription	Pancreas	Pancrea
41	chr11:64491600-64492800	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr11:64491600-64493000	Enhancers	Fetal Intestine Small	intestine
43	chr11:64491600-64493400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr11:64491600-64493600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr11:64491600-64493800	Enhancers	A549	lung
46	chr11:64491600-64494400	Enhancers	iPS-18 Cell Line	embryonic stem cell
47	chr11:64491600-64494800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr11:64491600-64499400	Weak transcription	Brain Anterior Caudate	brain
49	chr11:64491600-64502600	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr11:64491600-64503200	Weak transcription	Esophagus	oesophagus

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