Variant report

Variant	rs10840300
Chromosome Location	chr11:9796727-9796728
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	chr11:9796336-9796736	T-47D	breast:	n/a	n/a
2	JUND	chr11:9796144-9796980	SK-N-SH	brain:	n/a	n/a
3	ESR1	chr11:9796418-9796824	T-47D	breast:	n/a	n/a
4	TEAD4	chr11:9796244-9796982	SK-N-SH	brain:	n/a	chr11:9796373-9796382
5	ESR1	chr11:9796423-9796894	T-47D	breast:	n/a	n/a
6	GATA3	chr11:9795872-9797115	SK-N-SH	brain:	n/a	n/a
7	TEAD4	chr11:9796186-9796995	SK-N-SH	brain:	n/a	chr11:9796373-9796382
8	PBX3	chr11:9796173-9796938	SK-N-SH	brain:	n/a	n/a
9	RCOR1	chr11:9796314-9796767	Hela-S3	cervix:	n/a	n/a
10	TCF12	chr11:9796055-9797075	SK-N-SH	brain:	n/a	n/a
11	POLR2A	chr11:9796703-9797544	ProgFib	skin:	n/a	n/a
12	GATA3	chr11:9796174-9796768	MCF-7	breast:	n/a	n/a
13	TCF12	chr11:9796016-9797071	SK-N-SH	brain:	n/a	n/a
14	GATA3	chr11:9796291-9796857	T-47D	breast:	n/a	n/a
15	MAX	chr11:9796242-9797379	Hela-S3	cervix:	n/a	n/a
16	ESR1	chr11:9796509-9796870	T-47D	breast:	n/a	n/a
17	MEF2A	chr11:9796136-9796929	SK-N-SH	brain:	n/a	n/a
18	NFIC	chr11:9796245-9796919	SK-N-SH	brain:	n/a	chr11:9796601-9796617 chr11:9796600-9796617
19	MAX	chr11:9796134-9796911	SK-N-SH	brain:	n/a	n/a
20	EP300	chr11:9796188-9796947	SK-N-SH	brain:	n/a	n/a
21	POLR2A	chr11:9796139-9796774	U87	brain:	n/a	n/a
22	JUND	chr11:9796186-9797002	SK-N-SH	brain:	n/a	n/a
23	POLR2A	chr11:9796035-9796735	U87	brain:	n/a	n/a
24	EP300	chr11:9796393-9796855	T-47D	breast:	n/a	n/a
25	POLR2A	chr11:9796195-9796816	SK-N-SH	brain:	n/a	n/a
26	GATA3	chr11:9795990-9796976	SK-N-SH	brain:	n/a	n/a
27	GTF2F1	chr11:9796339-9796849	Hela-S3	cervix:	n/a	n/a
28	ESR1	chr11:9796409-9796803	T-47D	breast:	n/a	n/a
29	RFX5	chr11:9796355-9796788	Hela-S3	cervix:	n/a	n/a
30	RXRA	chr11:9796195-9796979	SK-N-SH	brain:	n/a	n/a
31	FOSL2	chr11:9796316-9796806	SK-N-SH	brain:	n/a	n/a
32	PBX3	chr11:9796191-9796989	SK-N-SH	brain:	n/a	n/a
33	EP300	chr11:9796051-9797004	SK-N-SH	brain:	n/a	n/a
34	EP300	chr11:9796379-9796869	T-47D	breast:	n/a	n/a
35	MYC	chr11:9796398-9797301	Hela-S3	cervix:	n/a	n/a
36	GATA3	chr11:9796382-9796813	MCF-7	breast:	n/a	n/a
37	FOSL2	chr11:9796196-9797099	SK-N-SH	brain:	n/a	n/a
38	NFIC	chr11:9796036-9796956	SK-N-SH	brain:	n/a	chr11:9796601-9796617 chr11:9796600-9796617

Variant related genes	Relation type
SBF2-AS1	TF binding region

Extended variants
information (count: 42 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1045634	0.93[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];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10770061	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[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	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10840302	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10840304	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10840307	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11042494	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11042495	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11042496	0.90[CEU][hapmap];0.94[EUR][1000 genomes]
rs11042498	0.89[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];0.82[MKK][hapmap];0.88[ASN][1000 genomes]
rs11828748	0.81[ASN][1000 genomes]
rs12786198	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1496475	0.80[JPT][hapmap]
rs16907071	0.89[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs2878800	0.80[JPT][hapmap]
rs360148	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs360149	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3751001	0.89[ASN][1000 genomes]
rs3763862	0.95[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs3829252	0.93[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];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4910500	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]
rs4910501	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4910502	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4910503	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4910505	0.96[CEU][hapmap];0.95[EUR][1000 genomes]
rs55934784	0.92[ASN][1000 genomes]
rs7102804	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7105203	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7113459	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7120754	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7124706	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7925875	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7936721	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9795085	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9795121	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9795122	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9795123	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[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
rs10840300	OR56A1	cis	cerebellum	SCAN
rs10840300	ASCL3	cis	parietal	SCAN
rs10840300	OR2D2	cis	cerebellum	SCAN
rs10840300	CCKBR	cis	cerebellum	SCAN
rs10840300	WEE1	cis	cerebellum	SCAN
rs10840300	OR56B4	cis	cerebellum	SCAN

Chromatin state (count:106 , 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	chr11:9784400-9797000	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr11:9787400-9796800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr11:9787400-9799000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr11:9787400-9801000	Weak transcription	Aorta	Aorta
19	chr11:9787600-9797600	Weak transcription	Fetal Intestine Large	intestine
20	chr11:9787600-9799200	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr11:9787600-9799200	Weak transcription	Fetal Lung	lung
22	chr11:9787800-9801000	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr11:9787800-9805200	Weak transcription	Colonic Mucosa	Colon
24	chr11:9788000-9801000	Weak transcription	Lung	lung
25	chr11:9788200-9801000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr11:9788600-9801600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr11:9788800-9799000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr11:9789200-9801000	Weak transcription	Spleen	Spleen
29	chr11:9789400-9798000	Weak transcription	Placenta	Placenta
30	chr11:9790200-9799200	Weak transcription	Adipose Nuclei	Adipose
31	chr11:9791000-9801000	Weak transcription	Primary neutrophils fromperipheralblood	blood
32	chr11:9792000-9801200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr11:9792200-9801000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr11:9792600-9798800	Weak transcription	Brain Germinal Matrix	brain
35	chr11:9792600-9799000	Weak transcription	Fetal Muscle Trunk	muscle
36	chr11:9793800-9801000	Weak transcription	Primary T cells fromperipheralblood	blood
37	chr11:9794200-9801000	Weak transcription	Fetal Intestine Small	intestine
38	chr11:9794400-9797000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr11:9795200-9797000	Enhancers	HSMM	muscle
40	chr11:9795200-9797200	Enhancers	NHDF-Ad	bronchial
41	chr11:9795200-9798000	Enhancers	NHLF	lung
42	chr11:9795200-9798600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr11:9795200-9812800	Strong transcription	Monocytes-CD14+_RO01746	blood
44	chr11:9795400-9797200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr11:9795400-9797600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr11:9795400-9798200	Enhancers	Osteobl	bone
47	chr11:9795400-9798800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr11:9795400-9798800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr11:9795600-9797200	Enhancers	Fetal Muscle Leg	muscle
50	chr11:9795600-9797400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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