Variant report

Variant	rs4910500
Chromosome Location	chr11:9797002-9797003
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	GATA3	chr11:9795872-9797115	SK-N-SH	brain:	n/a	n/a
2	TCF12	chr11:9796055-9797075	SK-N-SH	brain:	n/a	n/a
3	POLR2A	chr11:9796703-9797544	ProgFib	skin:	n/a	n/a
4	POLR2A	chr11:9796905-9797215	H1-hESC	embryonic stem cell:	n/a	n/a
5	TCF12	chr11:9796016-9797071	SK-N-SH	brain:	n/a	n/a
6	MAX	chr11:9796242-9797379	Hela-S3	cervix:	n/a	n/a
7	CEBPB	chr11:9796939-9797176	Hela-S3	cervix:	n/a	n/a
8	JUND	chr11:9796186-9797002	SK-N-SH	brain:	n/a	n/a
9	BRCA1	chr11:9796920-9797241	Hela-S3	cervix:	n/a	n/a
10	RCOR1	chr11:9796974-9797296	Hela-S3	cervix:	n/a	n/a
11	EP300	chr11:9796051-9797004	SK-N-SH	brain:	n/a	n/a
12	MYC	chr11:9796398-9797301	Hela-S3	cervix:	n/a	n/a
13	FOSL2	chr11:9796196-9797099	SK-N-SH	brain:	n/a	n/a

Variant related genes	Relation type
SBF2-AS1	TF binding region

Extended variants
information (count: 46 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs1045634	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1056593	0.80[JPT][hapmap]
rs10770061	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.95[MEX][hapmap];0.98[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]
rs10840300	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10840301	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10840302	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10840304	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10840307	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11042494	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11042495	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11042496	0.90[CEU][hapmap];0.95[EUR][1000 genomes]
rs11042497	0.80[EUR][1000 genomes]
rs11042498	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.81[MKK][hapmap];0.94[ASN][1000 genomes]
rs12786198	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1496475	0.85[JPT][hapmap]
rs1532422	0.85[JPT][hapmap]
rs16907071	0.94[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs2878800	0.85[JPT][hapmap]
rs360148	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs360149	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3751001	0.95[ASN][1000 genomes]
rs3763862	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs3829252	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4910501	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4910502	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4910503	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4910505	0.96[CEU][hapmap];0.96[EUR][1000 genomes]
rs55934784	0.98[ASN][1000 genomes]
rs7102804	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7105203	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7113055	0.84[JPT][hapmap]
rs7113459	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7114514	0.84[JPT][hapmap]
rs7120754	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7124706	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7925875	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7936721	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9795085	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9795121	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9795122	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9795123	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]

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	nsv933855	chr11:9645441-10130519	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers 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	40 gene(s)	inside rSNPs	diseases
2	nsv1053369	chr11:9647837-9876054	Genic enhancers Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv553468	chr11:9667828-9827871	Weak transcription Genic enhancers Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv896987	chr11:9759918-9885849	Strong transcription Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	esv3384280	chr11:9766350-9911228	Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4910500	ASCL3	cis	parietal	SCAN
rs4910500	WEE1	cis	cerebellum	SCAN
rs4910500	OR56B4	cis	cerebellum	SCAN
rs4910500	CCKBR	cis	cerebellum	SCAN
rs4910500	OR56A1	cis	cerebellum	SCAN
rs4910500	OR2D2	cis	cerebellum	SCAN

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:9780600-9813200	Weak transcription	Small Intestine	intestine
2	chr11:9781400-9800800	Weak transcription	Fetal Brain Female	brain
3	chr11:9781600-9798200	Weak transcription	Primary monocytes fromperipheralblood	blood
4	chr11:9781600-9801000	Weak transcription	Primary T cells from cord blood	blood
5	chr11:9781600-9809000	Weak transcription	Fetal Brain Male	brain
6	chr11:9781800-9799200	Weak transcription	Primary B cells from cord blood	blood
7	chr11:9781800-9799200	Weak transcription	Primary hematopoietic stem cells	blood
8	chr11:9781800-9801200	Weak transcription	Duodenum Mucosa	Duodenum
9	chr11:9781800-9801600	Weak transcription	Primary B cells from peripheral blood	blood
10	chr11:9782000-9798000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr11:9782400-9799400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr11:9782600-9797800	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr11:9784000-9797200	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr11:9784000-9801200	Weak transcription	Gastric	stomach
15	chr11:9787400-9799000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr11:9787400-9801000	Weak transcription	Aorta	Aorta
17	chr11:9787600-9797600	Weak transcription	Fetal Intestine Large	intestine
18	chr11:9787600-9799200	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr11:9787600-9799200	Weak transcription	Fetal Lung	lung
20	chr11:9787800-9801000	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr11:9787800-9805200	Weak transcription	Colonic Mucosa	Colon
22	chr11:9788000-9801000	Weak transcription	Lung	lung
23	chr11:9788200-9801000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr11:9788600-9801600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr11:9788800-9799000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr11:9789200-9801000	Weak transcription	Spleen	Spleen
27	chr11:9789400-9798000	Weak transcription	Placenta	Placenta
28	chr11:9790200-9799200	Weak transcription	Adipose Nuclei	Adipose
29	chr11:9791000-9801000	Weak transcription	Primary neutrophils fromperipheralblood	blood
30	chr11:9792000-9801200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr11:9792200-9801000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr11:9792600-9798800	Weak transcription	Brain Germinal Matrix	brain
33	chr11:9792600-9799000	Weak transcription	Fetal Muscle Trunk	muscle
34	chr11:9793800-9801000	Weak transcription	Primary T cells fromperipheralblood	blood
35	chr11:9794200-9801000	Weak transcription	Fetal Intestine Small	intestine
36	chr11:9795200-9797200	Enhancers	NHDF-Ad	bronchial
37	chr11:9795200-9798000	Enhancers	NHLF	lung
38	chr11:9795200-9798600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr11:9795200-9812800	Strong transcription	Monocytes-CD14+_RO01746	blood
40	chr11:9795400-9797200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr11:9795400-9797600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr11:9795400-9798200	Enhancers	Osteobl	bone
43	chr11:9795400-9798800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr11:9795400-9798800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr11:9795600-9797200	Enhancers	Fetal Muscle Leg	muscle
46	chr11:9795600-9797400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr11:9795600-9799000	Weak transcription	Fetal Stomach	stomach
48	chr11:9795800-9797200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
49	chr11:9795800-9797200	Enhancers	Placenta Amnion	Placenta Amnion
50	chr11:9795800-9799000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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