Variant report

Variant	rs73416199
Chromosome Location	chr11:9860656-9860657
allele	A/C
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	STAT3	chr11:9860418-9860863	MCF10A-Er-Src	breast:	n/a	n/a
2	MYC	chr11:9860390-9860833	MCF10A-Er-Src	breast:	n/a	n/a
3	NFIC	chr11:9860302-9860970	GM12878	blood:	n/a	n/a
4	FOS	chr11:9860501-9860674	MCF10A-Er-Src	breast:	n/a	n/a
5	BCLAF1	chr11:9860396-9860731	GM12878	blood:	n/a	chr11:9860433-9860442
6	POLR2A	chr11:9860374-9860848	PANC-1	pancreas:	n/a	n/a
7	PAX5	chr11:9860373-9860834	GM12878	blood:	n/a	chr11:9860433-9860442 chr11:9860793-9860802
8	BATF	chr11:9860392-9860752	GM12878	blood:	n/a	n/a
9	SP1	chr11:9860591-9860963	H1-hESC	embryonic stem cell:	n/a	n/a
10	FOS	chr11:9860403-9860761	MCF10A-Er-Src	breast:	n/a	n/a
11	BCL11A	chr11:9860463-9860683	GM12878	blood:	n/a	n/a
12	TCF3	chr11:9860469-9860667	GM12878	blood:	n/a	n/a
13	RELA	chr11:9860388-9860846	GM12891	blood:	n/a	n/a
14	FOS	chr11:9860421-9860731	MCF10A-Er-Src	breast:	n/a	n/a
15	GATA3	chr11:9860374-9860698	T-47D	breast:	n/a	n/a
16	IRF4	chr11:9860399-9860813	GM12878	blood:	n/a	n/a
17	NFIC	chr11:9860263-9860937	GM12878	blood:	n/a	n/a
18	IKZF1	chr11:9860485-9860807	GM12878	blood:	n/a	n/a
19	TCF7L2	chr11:9860289-9861186	PANC-1	pancreas:	n/a	n/a
20	TBL1XR1	chr11:9860386-9860771	GM12878	blood:	n/a	n/a
21	STAT3	chr11:9859838-9860762	MCF10A-Er-Src	breast:	n/a	chr11:9859986-9859995 chr11:9859985-9859994 chr11:9860281-9860289
22	IRF4	chr11:9860426-9860710	GM12878	blood:	n/a	n/a
23	BATF	chr11:9860401-9860780	GM12878	blood:	n/a	n/a
24	FOS	chr11:9859801-9860861	MCF10A-Er-Src	breast:	n/a	chr11:9859984-9859995 chr11:9859986-9859993 chr11:9859986-9859994 chr11:9859986-9859995
25	RUNX3	chr11:9860261-9860929	GM12878	blood:	n/a	n/a
26	POLR2A	chr11:9860375-9860817	PANC-1	pancreas:	n/a	n/a
27	MTA3	chr11:9860270-9860894	GM12878	blood:	n/a	n/a
28	RUNX3	chr11:9860287-9860900	GM12878	blood:	n/a	n/a
29	STAT3	chr11:9860380-9860777	MCF10A-Er-Src	breast:	n/a	n/a
30	ATF2	chr11:9860350-9860911	GM12878	blood:	n/a	n/a
31	EP300	chr11:9860479-9860699	GM12878	blood:	n/a	n/a
32	TCF3	chr11:9860477-9860696	GM12878	blood:	n/a	n/a
33	MEF2C	chr11:9860355-9860844	GM12878	blood:	n/a	n/a
34	EBF1	chr11:9860431-9860698	GM12878	blood:	n/a	n/a
35	MEF2A	chr11:9860378-9860809	GM12878	blood:	n/a	n/a
36	RELA	chr11:9860425-9860976	GM19099	blood:	n/a	n/a
37	BHLHE40	chr11:9860450-9860695	GM12878	blood:	n/a	n/a
38	SPI1	chr11:9860519-9860845	GM12891	blood:	n/a	n/a
39	BCL11A	chr11:9860414-9860736	GM12878	blood:	n/a	chr11:9860433-9860442
40	EP300	chr11:9860468-9860668	GM12878	blood:	n/a	n/a
41	EBF1	chr11:9860477-9860870	GM12878	blood:	n/a	n/a
42	FOXM1	chr11:9860347-9860846	GM12878	blood:	n/a	n/a
43	MYC	chr11:9860442-9860716	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:9849633..9851299-chr11:9859618..9861347,2	K562	blood:

Variant related genes	Relation type
ENSG00000255476	TF binding region
ENSG00000133812	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11821145	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11822070	1.00[AMR][1000 genomes]
rs11823024	1.00[AMR][1000 genomes]
rs11823620	1.00[AMR][1000 genomes]
rs11824133	1.00[AMR][1000 genomes]
rs11824944	1.00[AMR][1000 genomes]
rs11826573	1.00[AMR][1000 genomes]
rs55805230	1.00[AMR][1000 genomes]
rs56004091	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57233768	1.00[AMR][1000 genomes]
rs57297566	1.00[AMR][1000 genomes]
rs57735272	1.00[AMR][1000 genomes]
rs57948595	1.00[AMR][1000 genomes]
rs58024914	1.00[AMR][1000 genomes]
rs58717942	1.00[AMR][1000 genomes]
rs58982478	1.00[AMR][1000 genomes]
rs73402415	1.00[AMR][1000 genomes]
rs73406739	1.00[AMR][1000 genomes]
rs73412193	1.00[AMR][1000 genomes]
rs73412196	1.00[AMR][1000 genomes]
rs73414129	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73418575	1.00[AMR][1000 genomes]
rs73418583	1.00[AMR][1000 genomes]
rs73418601	1.00[AMR][1000 genomes]
rs73420636	1.00[AMR][1000 genomes]
rs73420638	1.00[AMR][1000 genomes]
rs73420639	1.00[AMR][1000 genomes]
rs73420640	1.00[AMR][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	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
4	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
5	esv2762895	chr11:9849511-9954549	Flanking Active TSS Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:9812200-9862200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr11:9818600-9881400	Weak transcription	Spleen	Spleen
3	chr11:9824200-9867600	Weak transcription	Psoas Muscle	Psoas
4	chr11:9826800-9868200	Weak transcription	Aorta	Aorta
5	chr11:9829600-9865600	Weak transcription	Gastric	stomach
6	chr11:9830000-9860800	Weak transcription	Primary T cells from cord blood	blood
7	chr11:9830000-9864400	Weak transcription	Esophagus	oesophagus
8	chr11:9830200-9863000	Weak transcription	Primary T cells fromperipheralblood	blood
9	chr11:9830400-9860800	Weak transcription	Rectal Smooth Muscle	rectum
10	chr11:9830400-9880400	Weak transcription	Thymus	Thymus
11	chr11:9830800-9865600	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr11:9830800-9866800	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr11:9830800-9880600	Weak transcription	Fetal Brain Male	brain
14	chr11:9833400-9868400	Weak transcription	Fetal Kidney	kidney
15	chr11:9833600-9878800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr11:9834200-9876600	Weak transcription	Brain Germinal Matrix	brain
17	chr11:9834600-9867400	Weak transcription	Brain Hippocampus Middle	brain
18	chr11:9834600-9877200	Weak transcription	Right Ventricle	heart
19	chr11:9837600-9863200	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr11:9837600-9885800	Weak transcription	Hela-S3	cervix
21	chr11:9838600-9879800	Weak transcription	Fetal Thymus	thymus
22	chr11:9848200-9877000	Weak transcription	HepG2	liver
23	chr11:9849000-9863000	Weak transcription	Ovary	ovary
24	chr11:9851200-9880000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr11:9851600-9875400	Weak transcription	Stomach Mucosa	stomach
26	chr11:9851600-9880400	Weak transcription	Small Intestine	intestine
27	chr11:9853000-9871600	Weak transcription	Fetal Intestine Small	intestine
28	chr11:9853400-9877400	Weak transcription	Brain Substantia Nigra	brain
29	chr11:9854000-9865600	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr11:9854000-9868400	Weak transcription	Lung	lung
31	chr11:9854000-9877400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr11:9854000-9880600	Weak transcription	Colonic Mucosa	Colon
33	chr11:9856600-9861000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr11:9856600-9880000	Weak transcription	Fetal Heart	heart
35	chr11:9856800-9861000	Weak transcription	Fetal Brain Female	brain
36	chr11:9856800-9865600	Weak transcription	Pancreas	Pancrea
37	chr11:9857800-9861400	Strong transcription	Primary monocytes fromperipheralblood	blood
38	chr11:9859000-9860800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr11:9859000-9861000	Weak transcription	Primary T helper cells fromperipheralblood	blood
40	chr11:9859000-9872800	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr11:9859600-9860800	Enhancers	Osteobl	bone
42	chr11:9859600-9861200	Enhancers	NHEK	skin
43	chr11:9859600-9862800	Enhancers	HSMM	muscle
44	chr11:9859600-9871400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr11:9859800-9861000	Enhancers	NH-A	brain
46	chr11:9859800-9861400	Enhancers	iPS-20b Cell Line	embryonic stem cell
47	chr11:9859800-9861400	Strong transcription	Primary hematopoietic stem cells	blood
48	chr11:9859800-9861400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr11:9859800-9861600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr11:9859800-9863800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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