Variant report

Variant	rs11820048
Chromosome Location	chr11:86012997-86012998
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	POLR2A	chr11:86012959-86013845	GM12892	blood:	n/a	n/a
2	NFIC	chr11:86012833-86013581	ECC-1	luminal epithelium:	n/a	chr11:86013171-86013199
3	YY1	chr11:86012995-86013875	ECC-1	luminal epithelium:	n/a	n/a
4	RUNX3	chr11:86012936-86013746	GM12878	blood:	n/a	n/a
5	HEY1	chr11:86012913-86013654	HepG2	liver:	n/a	n/a
6	POLR2A	chr11:86012981-86013875	ECC-1	luminal epithelium:	n/a	n/a
7	HA-E2F1	chr11:86012979-86013768	MCF-7	breast:	n/a	chr11:86013592-86013601
8	TEAD4	chr11:86012971-86014354	K562	blood:	n/a	n/a
9	ELF1	chr11:86012857-86013582	GM12878	blood:	n/a	chr11:86013268-86013277 chr11:86013267-86013278 chr11:86013265-86013278
10	YY1	chr11:86012991-86013797	ECC-1	luminal epithelium:	n/a	n/a
11	TCF12	chr11:86012951-86013755	ECC-1	luminal epithelium:	n/a	n/a
12	STAT5A	chr11:86012957-86013538	GM12878	blood:	n/a	chr11:86013163-86013172 chr11:86013157-86013177 chr11:86013162-86013171 chr11:86013163-86013171
13	TEAD4	chr11:86012881-86013516	HepG2	liver:	n/a	n/a
14	POLR2A	chr11:86012875-86014435	PBDE	blood:	n/a	n/a
15	MAX	chr11:86012981-86013879	SK-N-SH	brain:	n/a	n/a
16	BCLAF1	chr11:86012947-86013619	K562	blood:	n/a	n/a
17	POLR2A	chr11:86012778-86014162	MCF10A-Er-Src	breast:	n/a	n/a
18	BCLAF1	chr11:86012942-86013616	GM12878	blood:	n/a	n/a
19	BCLAF1	chr11:86012955-86013709	GM12878	blood:	n/a	chr11:86013611-86013620
20	POLR2A	chr11:86012979-86013677	K562	blood:	n/a	n/a
21	POLR2A	chr11:86012838-86013815	Hela-S3	cervix:	n/a	n/a
22	REST	chr11:86012993-86013525	HepG2	liver:	n/a	n/a
23	ETS1	chr11:86012927-86013575	GM12878	blood:	n/a	chr11:86013269-86013278 chr11:86013124-86013137 chr11:86013326-86013337 chr11:86013269-86013278 chr11:86013202-86013215 chr11:86013269-86013286 chr11:86013201-86013214
24	TAF1	chr11:86012975-86013734	ECC-1	luminal epithelium:	n/a	n/a
25	TBP	chr11:86012826-86014044	Hela-S3	cervix:	n/a	n/a
26	POLR2A	chr11:86012937-86014617	GM12878	blood:	n/a	n/a
27	CHD2	chr11:86012995-86013568	HepG2	liver:	n/a	n/a
28	POLR2A	chr11:86012938-86014033	GM12878	blood:	n/a	n/a
29	ETS1	chr11:86012864-86013564	A549	lung:	n/a	chr11:86013269-86013278 chr11:86013124-86013137 chr11:86013326-86013337 chr11:86013269-86013278 chr11:86013202-86013215 chr11:86013269-86013286 chr11:86013201-86013214
30	SIX5	chr11:86012959-86013449	K562	blood:	n/a	chr11:86013202-86013211 chr11:86013204-86013213
31	POLR2A	chr11:86012984-86013870	GM19193	blood:	n/a	n/a
32	CBX3	chr11:86012839-86013604	K562	blood:	n/a	n/a
33	EGR1	chr11:86012981-86013637	MCF-7	breast:	n/a	chr11:86013125-86013149 chr11:86013178-86013202 chr11:86013592-86013601
34	POLR2A	chr11:86012952-86013943	Hela-S3	cervix:	n/a	n/a
35	EP300	chr11:86012912-86014222	GM12878	blood:	n/a	chr11:86013270-86013277
36	MAFK	chr11:86012946-86013429	Hela-S3	cervix:	n/a	n/a
37	GABPA	chr11:86012847-86013896	SK-N-SH	brain:	n/a	chr11:86013591-86013605 chr11:86013588-86013602 chr11:86013591-86013600 chr11:86013591-86013602
38	POLR2A	chr11:86012933-86013636	HepG2	liver:	n/a	n/a
39	JUND	chr11:86012961-86014008	K562	blood:	n/a	n/a
40	NR2C2	chr11:86012982-86013843	HepG2	liver:	n/a	chr11:86013311-86013326 chr11:86013313-86013326
41	ELF1	chr11:86012848-86013914	HCT-116	colon:	n/a	chr11:86013268-86013277 chr11:86013267-86013278 chr11:86013265-86013278
42	POLR2A	chr11:86012961-86013813	GM15510	blood:	n/a	n/a
43	SP1	chr11:86012810-86013690	HCT-116	colon:	n/a	n/a
44	STAT3	chr11:86012944-86013364	MCF10A-Er-Src	breast:	n/a	chr11:86013163-86013172 chr11:86013157-86013177 chr11:86013161-86013172 chr11:86013162-86013171 chr11:86013163-86013171
45	MTA3	chr11:86012807-86013838	GM12878	blood:	n/a	n/a
46	PML	chr11:86012980-86013621	MCF-7	breast:	n/a	n/a
47	TAF1	chr11:86012866-86013887	ECC-1	luminal epithelium:	n/a	n/a
48	ELF1	chr11:86012964-86013628	K562	blood:	n/a	chr11:86013268-86013277 chr11:86013267-86013278 chr11:86013265-86013278
49	KAP1	chr11:86012943-86013677	HEK293	kidney:	n/a	n/a
50	POLR2A	chr11:86012917-86013731	PANC-1	pancreas:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:85955907..85958640-chr11:86011728..86014261,2	MCF-7	breast:
2	chr11:85978505..85980119-chr11:86012077..86014955,2	K562	blood:
3	chr11:86010873..86013514-chr11:86034864..86037459,2	K562	blood:

Variant related genes	Relation type
C11orf73	TF binding region
ENSG00000239856	Chromatin interaction
ENSG00000074266	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10751135	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs10792836	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs11234604	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11820262	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11820306	1.00[ASN][1000 genomes]
rs11822824	0.85[CHB][hapmap];1.00[CHD][hapmap];0.87[YRI][hapmap];0.86[ASN][1000 genomes]
rs11823273	1.00[EUR][1000 genomes]
rs11823516	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];1.00[ASN][1000 genomes]
rs11825208	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];1.00[ASN][1000 genomes]
rs11827234	1.00[EUR][1000 genomes]
rs2167611	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[JPT][hapmap];0.83[YRI][hapmap];0.97[ASN][1000 genomes]
rs2279047	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs3758879	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs3824953	1.00[CEU][hapmap]
rs57089989	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57331254	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs57381996	0.81[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs7106523	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs7115858	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.82[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7116227	0.95[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7118858	0.86[ASN][1000 genomes]
rs7129295	1.00[ASN][1000 genomes]
rs7924368	1.00[CEU][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7931249	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];1.00[ASN][1000 genomes]
rs7934320	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap]
rs7951357	0.83[CHD][hapmap];0.89[JPT][hapmap]
rs7951433	0.83[CHD][hapmap];1.00[TSI][hapmap]
rs7951478	0.85[CHB][hapmap];0.89[JPT][hapmap];0.87[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832223	chr11:85845315-86015957	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv508643	chr11:85988577-86047719	Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	nsv519914	chr11:86010789-86013361	Enhancers Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:85995800-86013200	Weak transcription	Esophagus	oesophagus
2	chr11:85995800-86013200	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr11:85996000-86013000	Weak transcription	Fetal Intestine Large	intestine
4	chr11:86003200-86013000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr11:86012200-86013000	Flanking Active TSS	Dnd41	blood
6	chr11:86012200-86014800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr11:86012600-86013000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr11:86012600-86013000	Flanking Active TSS	Brain Anterior Caudate	brain
9	chr11:86012600-86013000	Flanking Active TSS	Brain Cingulate Gyrus	brain
10	chr11:86012600-86013000	Flanking Active TSS	Brain Hippocampus Middle	brain
11	chr11:86012600-86013000	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
12	chr11:86012600-86013000	Flanking Active TSS	Fetal Brain Female	brain
13	chr11:86012600-86013000	Flanking Active TSS	Hela-S3	cervix
14	chr11:86012600-86013400	Active TSS	HepG2	liver
15	chr11:86012600-86013600	Active TSS	Primary B cells from cord blood	blood
16	chr11:86012600-86013800	Active TSS	Brain Inferior Temporal Lobe	brain
17	chr11:86012600-86013800	Active TSS	Brain Substantia Nigra	brain
18	chr11:86012600-86014000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr11:86012600-86014000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr11:86012600-86014000	Active TSS	Brain Angular Gyrus	brain
21	chr11:86012600-86014000	Active TSS	Colon Smooth Muscle	Colon
22	chr11:86012600-86014200	Active TSS	Primary hematopoietic stem cells short term culture	blood
23	chr11:86012600-86014200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr11:86012600-86014200	Active TSS	NHLF	lung
25	chr11:86012600-86014400	Active TSS	ES-I3 Cell Line	embryonic stem cell
26	chr11:86012600-86014400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr11:86012600-86014400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr11:86012600-86014400	Active TSS	Brain Germinal Matrix	brain
29	chr11:86012600-86014400	Active TSS	Fetal Kidney	kidney
30	chr11:86012600-86014400	Active TSS	HMEC	breast
31	chr11:86012600-86014600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr11:86012600-86014600	Active TSS	HUES6 Cell Line	embryonic stem cell
33	chr11:86012600-86014600	Active TSS	iPS-15b Cell Line	embryonic stem cell
34	chr11:86012600-86014600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr11:86012600-86015200	Active TSS	K562	blood
36	chr11:86012800-86013000	Enhancers	Primary monocytes fromperipheralblood	blood
37	chr11:86012800-86013000	Enhancers	Primary B cells from peripheral blood	blood
38	chr11:86012800-86013000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
39	chr11:86012800-86013000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
40	chr11:86012800-86013000	Active TSS	Primary T helper naive cells fromperipheralblood	blood
41	chr11:86012800-86013000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
42	chr11:86012800-86013000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
43	chr11:86012800-86013000	Enhancers	Primary T helper cells fromperipheralblood	blood
44	chr11:86012800-86013000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
45	chr11:86012800-86013000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
46	chr11:86012800-86013000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
47	chr11:86012800-86013000	Enhancers	Fetal Intestine Small	intestine
48	chr11:86012800-86013000	Flanking Active TSS	Fetal Lung	lung
49	chr11:86012800-86013000	Enhancers	Rectal Smooth Muscle	rectum
50	chr11:86012800-86013000	Enhancers	Monocytes-CD14+_RO01746	blood

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