Variant report

Variant	rs3920052
Chromosome Location	chr11:86013899-86013900
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	SMARCC2	chr11:86013016-86013906	Hela-S3	cervix:	n/a	chr11:86013204-86013213
2	POLR2A	chr11:86013045-86014019	PANC-1	pancreas:	n/a	n/a
3	CUX1	chr11:86013027-86014241	K562	blood:	n/a	n/a
4	TEAD4	chr11:86012971-86014354	K562	blood:	n/a	n/a
5	POLR2A	chr11:86012875-86014435	PBDE	blood:	n/a	n/a
6	WRNIP1	chr11:86013002-86014128	GM12878	blood:	n/a	n/a
7	POLR2A	chr11:86012778-86014162	MCF10A-Er-Src	breast:	n/a	n/a
8	TBP	chr11:86012826-86014044	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr11:86012937-86014617	GM12878	blood:	n/a	n/a
10	POLR2A	chr11:86012938-86014033	GM12878	blood:	n/a	n/a
11	POLR2A	chr11:86012952-86013943	Hela-S3	cervix:	n/a	n/a
12	EP300	chr11:86012912-86014222	GM12878	blood:	n/a	chr11:86013270-86013277
13	YY1	chr11:86013021-86013961	SK-N-SH	brain:	n/a	n/a
14	POLR2A	chr11:86013070-86013914	GM12891	blood:	n/a	n/a
15	JUND	chr11:86012961-86014008	K562	blood:	n/a	n/a
16	ELF1	chr11:86012848-86013914	HCT-116	colon:	n/a	chr11:86013268-86013277 chr11:86013267-86013278 chr11:86013265-86013278
17	POLR2A	chr11:86012985-86013910	GM18505	blood:	n/a	n/a
18	MXI1	chr11:86012954-86013996	Hela-S3	cervix:	n/a	n/a
19	POLR2A	chr11:86012948-86013903	Hela-S3	cervix:	n/a	n/a
20	POLR2A	chr11:86012976-86013943	HepG2	liver:	n/a	n/a
21	IRF1	chr11:86012967-86014170	K562	blood:	n/a	chr11:86013305-86013314 chr11:86014068-86014075
22	SIX5	chr11:86012714-86014048	A549	lung:	n/a	chr11:86013202-86013211 chr11:86013204-86013213
23	POLR2A	chr11:86012923-86014602	GM19099	blood:	n/a	n/a
24	USF2	chr11:86013086-86013908	Hela-S3	cervix:	n/a	n/a
25	ARID3A	chr11:86012970-86013907	HepG2	liver:	n/a	n/a
26	POLR2A	chr11:86012928-86014010	K562	blood:	n/a	n/a
27	GABPA	chr11:86012668-86014011	A549	lung:	n/a	chr11:86013591-86013605 chr11:86013588-86013602 chr11:86013591-86013600 chr11:86013591-86013602
28	POLR2A	chr11:86012874-86013974	SK-N-SH	brain:	n/a	n/a
29	POLR2A	chr11:86012987-86013920	K562	blood:	n/a	n/a
30	RCOR1	chr11:86012986-86013901	Hela-S3	cervix:	n/a	n/a
31	SREBP1	chr11:86012339-86014954	GM12878	blood:	n/a	n/a
32	POLR2A	chr11:86012750-86014041	HUVEC	blood vessel:	n/a	n/a
33	POLR2A	chr11:86013761-86013993	HUVEC	blood vessel:	n/a	n/a
34	GABPA	chr11:86012547-86014185	MCF-7	breast:	n/a	chr11:86013591-86013605 chr11:86013588-86013602 chr11:86013591-86013600 chr11:86013591-86013602
35	POLR2A	chr11:86012949-86013999	GM12878	blood:	n/a	n/a
36	GATA1	chr11:86012964-86014523	PBDE	blood:	n/a	chr11:86014413-86014422
37	ZMIZ1	chr11:86013062-86014046	K562	blood:	n/a	n/a
38	MYC	chr11:86012993-86013962	K562	blood:	n/a	n/a
39	SIN3A	chr11:86012884-86013950	H1-hESC	embryonic stem cell:	n/a	n/a
40	SIN3AK20	chr11:86012724-86014053	MCF-7	breast:	n/a	n/a
41	SRF	chr11:86012792-86013913	HCT-116	colon:	n/a	chr11:86013486-86013500
42	POLR2A	chr11:86012972-86013931	GM12892	blood:	n/a	n/a
43	POLR2A	chr11:86013017-86013909	GM12878	blood:	n/a	n/a
44	POLR2A	chr11:86012967-86014064	GM12892	blood:	n/a	n/a
45	TBP	chr11:86013004-86014017	K562	blood:	n/a	n/a
46	RFX5	chr11:86013855-86014302	K562	blood:	n/a	chr11:86014229-86014244 chr11:86014229-86014244
47	POLR2A	chr11:86012890-86014036	ProgFib	skin:	n/a	n/a
48	POLR2A	chr11:86012960-86013960	HepG2	liver:	n/a	n/a
49	POLR2A	chr11:86012918-86014025	SK-N-MC	brain:	n/a	n/a
50	TAL1	chr11:86012974-86014341	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:85954509..85956884-chr11:86013356..86015049,2	K562	blood:
2	chr11:85374267..85376584-chr11:86013241..86015955,2	MCF-7	breast:
3	chr11:85955907..85958640-chr11:86011728..86014261,2	MCF-7	breast:
4	chr11:85978505..85980119-chr11:86012077..86014955,2	K562	blood:

Variant related genes	Relation type
C11orf73	TF binding region
ENSG00000137504	Chromatin interaction
ENSG00000074266	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11822620	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];0.97[ASN][1000 genomes]
rs11822899	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12417008	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12422031	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17210182	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17210189	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17210259	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17210343	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.83[MKK][hapmap];0.94[ASN][1000 genomes]
rs17210350	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];0.94[ASN][1000 genomes]
rs17210546	1.00[EUR][1000 genomes]
rs17817610	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17817659	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17817701	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17817719	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2036187	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2374703	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2374704	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34602206	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4474462	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59478404	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61039312	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7104068	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7105530	1.00[EUR][1000 genomes]
rs7114903	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7115094	1.00[EUR][1000 genomes]
rs7116376	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7116719	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7939108	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7944685	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:86012200-86014800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr11:86012600-86014000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr11:86012600-86014000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr11:86012600-86014000	Active TSS	Brain Angular Gyrus	brain
5	chr11:86012600-86014000	Active TSS	Colon Smooth Muscle	Colon
6	chr11:86012600-86014200	Active TSS	Primary hematopoietic stem cells short term culture	blood
7	chr11:86012600-86014200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr11:86012600-86014200	Active TSS	NHLF	lung
9	chr11:86012600-86014400	Active TSS	ES-I3 Cell Line	embryonic stem cell
10	chr11:86012600-86014400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr11:86012600-86014400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr11:86012600-86014400	Active TSS	Brain Germinal Matrix	brain
13	chr11:86012600-86014400	Active TSS	Fetal Kidney	kidney
14	chr11:86012600-86014400	Active TSS	HMEC	breast
15	chr11:86012600-86014600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr11:86012600-86014600	Active TSS	HUES6 Cell Line	embryonic stem cell
17	chr11:86012600-86014600	Active TSS	iPS-15b Cell Line	embryonic stem cell
18	chr11:86012600-86014600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr11:86012600-86015200	Active TSS	K562	blood
20	chr11:86012800-86014000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr11:86012800-86014000	Active TSS	Cortex derived primary cultured neurospheres	brain
22	chr11:86012800-86014000	Active TSS	Duodenum Smooth Muscle	Duodenum
23	chr11:86012800-86014000	Active TSS	Fetal Brain Male	brain
24	chr11:86012800-86014000	Active TSS	Pancreatic Islets	Pancreatic Islet
25	chr11:86012800-86014000	Active TSS	Rectal Mucosa Donor 31	rectum
26	chr11:86012800-86014000	Active TSS	Skeletal Muscle Male	skeletal muscle
27	chr11:86012800-86014000	Active TSS	Skeletal Muscle Female	skeletal muscle
28	chr11:86012800-86014000	Active TSS	NH-A	brain
29	chr11:86012800-86014200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr11:86012800-86014200	Active TSS	iPS-18 Cell Line	embryonic stem cell
31	chr11:86012800-86014200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr11:86012800-86014200	Active TSS	Fetal Stomach	stomach
33	chr11:86012800-86014200	Active TSS	HSMM	muscle
34	chr11:86012800-86014200	Active TSS	HUVEC	blood vessel
35	chr11:86012800-86014400	Active TSS	HUES48 Cell Line	embryonic stem cell
36	chr11:86012800-86014400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr11:86012800-86014400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr11:86012800-86014400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr11:86012800-86014400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr11:86012800-86014400	Active TSS	Fetal Muscle Leg	muscle
41	chr11:86012800-86014400	Active TSS	Fetal Thymus	thymus
42	chr11:86012800-86014400	Active TSS	Thymus	Thymus
43	chr11:86012800-86014400	Active TSS	A549	lung
44	chr11:86012800-86014400	Active TSS	HSMMtube	muscle
45	chr11:86012800-86014400	Active TSS	NHDF-Ad	bronchial
46	chr11:86012800-86014600	Active TSS	H1 Cell Line	embryonic stem cell
47	chr11:86012800-86014600	Active TSS	Psoas Muscle	Psoas
48	chr11:86012800-86014600	Active TSS	Right Atrium	heart
49	chr11:86012800-86014600	Active TSS	Stomach Smooth Muscle	stomach
50	chr11:86012800-86014800	Active TSS	iPS-20b Cell Line	embryonic stem cell

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