Variant report

Variant	rs575797
Chromosome Location	chr11:66408033-66408034
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:29)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:29 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:66405238-66408285	U87	brain:	n/a	n/a
2	POLR2A	chr11:66407668-66408496	K562	blood:	n/a	n/a
3	POLR2A	chr11:66404832-66408589	PFSK-1	brain:	n/a	n/a
4	POLR2A	chr11:66404758-66409916	PANC-1	pancreas:	n/a	n/a
5	POLR2A	chr11:66404691-66408516	GM12891	blood:	n/a	n/a
6	POLR2A	chr11:66407853-66408406	GM12891	blood:	n/a	n/a
7	POLR2A	chr11:66407899-66408531	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr11:66404803-66409178	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr11:66408028-66408280	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr11:66404751-66409197	GM12878	blood:	n/a	n/a
11	POLR2A	chr11:66407627-66409148	GM12878	blood:	n/a	n/a
12	POLR2A	chr11:66408012-66408085	MCF-7	breast:	n/a	n/a
13	POLR2A	chr11:66407947-66408311	U87	brain:	n/a	n/a
14	POLR2A	chr11:66404700-66409319	SK-N-MC	brain:	n/a	n/a
15	POLR2A	chr11:66404827-66409201	GM12892	blood:	n/a	n/a
16	WRNIP1	chr11:66407567-66408543	GM12878	blood:	n/a	n/a
17	POLR2A	chr11:66407602-66409113	HepG2	liver:	n/a	n/a
18	POLR2A	chr11:66405184-66409193	GM12891	blood:	n/a	n/a
19	POLR2A	chr11:66405295-66408618	GM12891	blood:	n/a	n/a
20	POLR2A	chr11:66404698-66409288	GM12892	blood:	n/a	n/a
21	TBL1XR1	chr11:66407787-66408047	K562	blood:	n/a	n/a
22	POLR2A	chr11:66407443-66408583	K562	blood:	n/a	n/a
23	POLR2A	chr11:66407872-66408490	GM12892	blood:	n/a	n/a
24	POLR2A	chr11:66407452-66415502	HepG2	liver:	n/a	n/a
25	POLR2A	chr11:66404807-66408589	GM12878	blood:	n/a	n/a
26	POLR2A	chr11:66407613-66408311	U87	brain:	n/a	n/a
27	POLR2A	chr11:66407905-66408170	Hela-S3	cervix:	n/a	n/a
28	POLR2A	chr11:66404694-66409669	GM12892	blood:	n/a	n/a
29	POLR2A	chr11:66407672-66408508	K562	blood:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:66405952..66409597-chr11:66443012..66447533,6	MCF-7	breast:
2	chr11:66407180..66409474-chr11:66600961..66602936,2	K562	blood:
3	chr11:66312205..66315427-chr11:66405180..66408532,5	MCF-7	breast:
4	chr11:66407739..66410273-chr11:66444249..66447501,5	K562	blood:
5	chr11:66406313..66408436-chr17:74731744..74733965,2	K562	blood:
6	chr11:66358667..66365231-chr11:66403397..66409781,9	K562	blood:
7	chr11:66405423..66410273-chr11:66443859..66447584,9	K562	blood:
8	chr11:66405112..66408239-chr11:66443909..66446987,4	MCF-7	breast:
9	chr11:66406543..66408632-chr11:66427467..66429685,2	K562	blood:

No data

Variant related genes	Relation type
RBM4	TF binding region
ENSG00000173914	Chromatin interaction
ENSG00000248746	Chromatin interaction
ENSG00000173992	Chromatin interaction
ENSG00000092931	Chromatin interaction
ENSG00000182791	Chromatin interaction
ENSG00000207556	Chromatin interaction
ENSG00000174165	Chromatin interaction
ENSG00000161547	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11227596	0.82[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs13897	1.00[ASW][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs17065	0.82[CHB][hapmap]
rs17147749	1.00[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs17496250	0.90[CHB][hapmap]
rs2290463	1.00[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs3737525	0.82[CHB][hapmap]
rs3782079	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3816492	0.82[CHB][hapmap]
rs45625436	1.00[AFR][1000 genomes]
rs477335	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs478807	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs479261	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs519380	0.82[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs527550	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55662252	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs563344	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56680801	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56848911	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs57206977	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs57220229	0.87[AMR][1000 genomes]
rs573673	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60084486	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60395535	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs623022	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs639938	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs645307	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs648491	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[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	nsv522277	chr11:66234023-66493825	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
2	nsv897789	chr11:66372390-66634397	Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	117 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:66406200-66410200	Transcr. at gene 5' and 3'	Dnd41	blood
2	chr11:66406200-66410400	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
3	chr11:66406200-66410400	Transcr. at gene 5' and 3'	Rectal Smooth Muscle	rectum
4	chr11:66406200-66410600	Transcr. at gene 5' and 3'	Primary T regulatory cells fromperipheralblood	blood
5	chr11:66406200-66411000	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
6	chr11:66406600-66408600	Transcr. at gene 5' and 3'	Duodenum Smooth Muscle	Duodenum
7	chr11:66406600-66409800	Transcr. at gene 5' and 3'	K562	blood
8	chr11:66406600-66410400	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr11:66406800-66410400	Transcr. at gene 5' and 3'	HMEC	breast
10	chr11:66406800-66410600	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
11	chr11:66406800-66411200	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr11:66406800-66411200	Transcr. at gene 5' and 3'	Fetal Lung	lung
13	chr11:66406800-66411800	Transcr. at gene 5' and 3'	HSMM	muscle
14	chr11:66406800-66413000	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
15	chr11:66407000-66409200	Transcr. at gene 5' and 3'	Fetal Intestine Large	intestine
16	chr11:66407000-66409600	Transcr. at gene 5' and 3'	Fetal Muscle Leg	muscle
17	chr11:66407000-66409600	Transcr. at gene 5' and 3'	A549	lung
18	chr11:66407000-66409800	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
19	chr11:66407000-66410000	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr11:66407000-66410600	Transcr. at gene 5' and 3'	iPS-18 Cell Line	embryonic stem cell
21	chr11:66407000-66411600	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
22	chr11:66407000-66411800	Transcr. at gene 5' and 3'	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr11:66407000-66413600	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
24	chr11:66407000-66434400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr11:66407200-66408200	Flanking Active TSS	Fetal Heart	heart
26	chr11:66407200-66408200	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
27	chr11:66407200-66408200	Genic enhancers	Small Intestine	intestine
28	chr11:66407200-66408400	Genic enhancers	Spleen	Spleen
29	chr11:66407200-66408600	Transcr. at gene 5' and 3'	Fetal Stomach	stomach
30	chr11:66407200-66408800	Transcr. at gene 5' and 3'	NHLF	lung
31	chr11:66407200-66409200	Transcr. at gene 5' and 3'	Monocytes-CD14+_RO01746	blood
32	chr11:66407200-66409800	Transcr. at gene 5' and 3'	H1 Cell Line	embryonic stem cell
33	chr11:66407200-66409800	Genic enhancers	Primary monocytes fromperipheralblood	blood
34	chr11:66407200-66409800	Transcr. at gene 5' and 3'	Fetal Thymus	thymus
35	chr11:66407200-66409800	Transcr. at gene 5' and 3'	Thymus	Thymus
36	chr11:66407200-66410200	Transcr. at gene 5' and 3'	Primary T helper naive cells fromperipheralblood	blood
37	chr11:66407200-66410400	Transcr. at gene 5' and 3'	HUES48 Cell Line	embryonic stem cell
38	chr11:66407200-66410400	Transcr. at gene 5' and 3'	HUVEC	blood vessel
39	chr11:66407200-66410400	Transcr. at gene 5' and 3'	NHEK	skin
40	chr11:66407200-66411800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
41	chr11:66407200-66411800	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
42	chr11:66407200-66413000	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr11:66407200-66413000	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
44	chr11:66407200-66413600	Genic enhancers	Primary B cells from peripheral blood	blood
45	chr11:66407200-66413800	Genic enhancers	Sigmoid Colon	Sigmoid Colon
46	chr11:66407400-66408200	Transcr. at gene 5' and 3'	Brain Hippocampus Middle	brain
47	chr11:66407400-66408200	Transcr. at gene 5' and 3'	Brain Substantia Nigra	brain
48	chr11:66407400-66408200	Transcr. at gene 5' and 3'	Colon Smooth Muscle	Colon
49	chr11:66407400-66408200	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
50	chr11:66407400-66408200	Transcr. at gene 5' and 3'	Stomach Smooth Muscle	stomach

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