Variant report

Variant	rs9971601
Chromosome Location	chr11:9796292-9796293
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	JUND	chr11:9796144-9796980	SK-N-SH	brain:	n/a	n/a
2	TEAD4	chr11:9796244-9796982	SK-N-SH	brain:	n/a	chr11:9796373-9796382
3	GATA3	chr11:9795872-9797115	SK-N-SH	brain:	n/a	n/a
4	TEAD4	chr11:9796186-9796995	SK-N-SH	brain:	n/a	chr11:9796373-9796382
5	PBX3	chr11:9796173-9796938	SK-N-SH	brain:	n/a	n/a
6	TCF12	chr11:9796055-9797075	SK-N-SH	brain:	n/a	n/a
7	GATA3	chr11:9796174-9796768	MCF-7	breast:	n/a	n/a
8	TCF12	chr11:9796016-9797071	SK-N-SH	brain:	n/a	n/a
9	GATA3	chr11:9796291-9796857	T-47D	breast:	n/a	n/a
10	MAX	chr11:9796242-9797379	Hela-S3	cervix:	n/a	n/a
11	MEF2A	chr11:9796136-9796929	SK-N-SH	brain:	n/a	n/a
12	NFIC	chr11:9796245-9796919	SK-N-SH	brain:	n/a	chr11:9796601-9796617 chr11:9796600-9796617
13	MAX	chr11:9796134-9796911	SK-N-SH	brain:	n/a	n/a
14	EP300	chr11:9796188-9796947	SK-N-SH	brain:	n/a	n/a
15	CTCF	chr11:9796180-9796330	AG04449	skin:	n/a	n/a
16	POLR2A	chr11:9796139-9796774	U87	brain:	n/a	n/a
17	JUND	chr11:9796186-9797002	SK-N-SH	brain:	n/a	n/a
18	POLR2A	chr11:9796139-9796616	U87	brain:	n/a	n/a
19	POLR2A	chr11:9796035-9796735	U87	brain:	n/a	n/a
20	POLR2A	chr11:9796195-9796816	SK-N-SH	brain:	n/a	n/a
21	POLR2A	chr11:9796055-9796580	ProgFib	skin:	n/a	n/a
22	GATA3	chr11:9795990-9796976	SK-N-SH	brain:	n/a	n/a
23	RXRA	chr11:9796195-9796979	SK-N-SH	brain:	n/a	n/a
24	PBX3	chr11:9796191-9796989	SK-N-SH	brain:	n/a	n/a
25	EP300	chr11:9796051-9797004	SK-N-SH	brain:	n/a	n/a
26	FOSL2	chr11:9796196-9797099	SK-N-SH	brain:	n/a	n/a
27	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: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs11042504	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11042508	1.00[EUR][1000 genomes]
rs11042513	1.00[EUR][1000 genomes]
rs11042520	1.00[EUR][1000 genomes]
rs11042522	1.00[EUR][1000 genomes]
rs11042537	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11042538	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11042544	1.00[AMR][1000 genomes]
rs11042546	1.00[AMR][1000 genomes]
rs11042551	1.00[AMR][1000 genomes]
rs12270313	1.00[EUR][1000 genomes]
rs12270444	1.00[AMR][1000 genomes]
rs12270596	1.00[AMR][1000 genomes]
rs12285985	1.00[EUR][1000 genomes]
rs12290340	0.85[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12291871	0.91[LWK][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12294282	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12295264	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13377319	1.00[AMR][1000 genomes]
rs13377352	1.00[ASW][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs360121	1.00[EUR][1000 genomes]
rs57108291	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57125659	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57460369	1.00[EUR][1000 genomes]
rs57669768	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60528623	1.00[EUR][1000 genomes]
rs7116821	1.00[EUR][1000 genomes]
rs73408245	1.00[AMR][1000 genomes]
rs7358421	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7358470	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9630162	1.00[AMR][1000 genomes];1.00[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

No data

Chromatin state (count:92 , 50 per page) page: 1 2

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	chr11:9788000-9796600	Weak transcription	Pancreas	Pancrea
25	chr11:9788000-9801000	Weak transcription	Lung	lung
26	chr11:9788200-9801000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr11:9788600-9796600	Weak transcription	Fetal Heart	heart
28	chr11:9788600-9801600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr11:9788800-9799000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr11:9789200-9801000	Weak transcription	Spleen	Spleen
31	chr11:9789400-9798000	Weak transcription	Placenta	Placenta
32	chr11:9790200-9799200	Weak transcription	Adipose Nuclei	Adipose
33	chr11:9791000-9801000	Weak transcription	Primary neutrophils fromperipheralblood	blood
34	chr11:9792000-9801200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr11:9792200-9801000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
36	chr11:9792600-9798800	Weak transcription	Brain Germinal Matrix	brain
37	chr11:9792600-9799000	Weak transcription	Fetal Muscle Trunk	muscle
38	chr11:9793800-9801000	Weak transcription	Primary T cells fromperipheralblood	blood
39	chr11:9794200-9801000	Weak transcription	Fetal Intestine Small	intestine
40	chr11:9794400-9797000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr11:9795200-9796400	Enhancers	HSMMtube	muscle
42	chr11:9795200-9797000	Enhancers	HSMM	muscle
43	chr11:9795200-9797200	Enhancers	NHDF-Ad	bronchial
44	chr11:9795200-9798000	Enhancers	NHLF	lung
45	chr11:9795200-9798600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr11:9795200-9812800	Strong transcription	Monocytes-CD14+_RO01746	blood
47	chr11:9795400-9797200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr11:9795400-9797600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr11:9795400-9798200	Enhancers	Osteobl	bone
50	chr11:9795400-9798800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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