Variant report

Variant	rs6592523
Chromosome Location	chr11:73109877-73109878
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	chr11:73108592-73110675	GM12878	blood:	n/a	n/a
2	POLR2A	chr11:73108641-73110955	GM12878	blood:	n/a	n/a
3	POLR2A	chr11:73102033-73111863	GM12892	blood:	n/a	n/a
4	POLR2A	chr11:73109165-73110972	GM12891	blood:	n/a	n/a
5	POLR2A	chr11:73109767-73110176	ECC-1	luminal epithelium:	n/a	n/a
6	POLR2A	chr11:73108680-73111011	GM12878	blood:	n/a	n/a
7	POLR2A	chr11:73108657-73110882	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr11:73098106-73111810	GM12878	blood:	n/a	n/a
9	POLR2A	chr11:73108667-73110883	PANC-1	pancreas:	n/a	n/a
10	POLR2A	chr11:73108583-73111066	GM12891	blood:	n/a	n/a
11	POLR2A	chr11:73109434-73110464	HepG2	liver:	n/a	n/a
12	PML	chr11:73109869-73111090	GM12878	blood:	n/a	chr11:73110458-73110467 chr11:73110773-73110781
13	POLR2A	chr11:73105208-73111038	GM12878	blood:	n/a	n/a
14	POLR2A	chr11:73109467-73110452	GM12891	blood:	n/a	n/a
15	POLR2A	chr11:73103307-73110889	A549	lung:	n/a	n/a
16	FOSL2	chr11:73109527-73110782	HepG2	liver:	n/a	chr11:73110459-73110469 chr11:73110459-73110469 chr11:73110458-73110470 chr11:73110460-73110468 chr11:73110459-73110469
17	POLR2A	chr11:73108052-73111038	GM12892	blood:	n/a	n/a
18	POLR2A	chr11:73109535-73110201	H1-hESC	embryonic stem cell:	n/a	n/a
19	POLR2A	chr11:73109830-73110014	HUVEC	blood vessel:	n/a	n/a
20	POLR2A	chr11:73109860-73110513	H1-neurons	neurons:	n/a	n/a
21	POLR2A	chr11:73109338-73110064	H1-hESC	embryonic stem cell:	n/a	n/a
22	POLR2A	chr11:73108392-73111835	PANC-1	pancreas:	n/a	n/a
23	POLR2A	chr11:73109203-73110633	GM12878	blood:	n/a	n/a
24	POLR2A	chr11:73108814-73110512	H1-hESC	embryonic stem cell:	n/a	n/a
25	NFATC1	chr11:73109708-73110110	GM12878	blood:	n/a	n/a
26	POLR2A	chr11:73109729-73110202	HCT-116	colon:	n/a	n/a
27	POLR2A	chr11:73108577-73111096	Hela-S3	cervix:	n/a	n/a
28	POLR2A	chr11:73103211-73111119	GM12892	blood:	n/a	n/a
29	POLR2A	chr11:73108603-73111057	PFSK-1	brain:	n/a	n/a
30	POLR2A	chr11:73109730-73109916	SK-N-SH	brain:	n/a	n/a
31	POLR2A	chr11:73109646-73110664	SK-N-SH	brain:	n/a	n/a
32	POLR2A	chr11:73108638-73111006	K562	blood:	n/a	n/a
33	POLR2A	chr11:73108012-73111145	HL-60	blood:	n/a	n/a
34	POLR2A	chr11:73108545-73110982	GM12891	blood:	n/a	n/a
35	POLR2A	chr11:73109395-73110727	Hela-S3	cervix:	n/a	n/a
36	POLR2A	chr11:73108761-73110918	GM18505	blood:	n/a	n/a
37	POLR2A	chr11:73109567-73110001	Hela-S3	cervix:	n/a	n/a
38	POU2F2	chr11:73109642-73110565	GM12891	blood:	n/a	n/a
39	NFATC1	chr11:73109657-73110412	GM12878	blood:	n/a	n/a
40	POLR2A	chr11:73107978-73111022	GM12891	blood:	n/a	n/a
41	POLR2A	chr11:73103383-73111849	GM12892	blood:	n/a	n/a
42	POLR2A	chr11:73109199-73111058	K562	blood:	n/a	n/a
43	POLR2A	chr11:73109146-73110686	K562	blood:	n/a	n/a
44	MTA3	chr11:73109539-73109925	GM12878	blood:	n/a	n/a
45	POLR2A	chr11:73108632-73111915	SK-N-MC	brain:	n/a	n/a
46	POLR2A	chr11:73108683-73110163	GM12878	blood:	n/a	n/a
47	POLR2A	chr11:73109477-73110768	H1-neurons	neurons:	n/a	n/a
48	POLR2A	chr11:73109057-73110874	PFSK-1	brain:	n/a	n/a
49	POLR2A	chr11:73108703-73110882	GM19193	blood:	n/a	n/a
50	POLR2A	chr11:73108626-73111033	HL-60	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:73109121..73112181-chr11:73112375..73115305,3	MCF-7	breast:
2	chr11:73056183..73058229-chr11:73108925..73110683,2	MCF-7	breast:
3	chr11:73085933..73089159-chr11:73107371..73110005,3	MCF-7	breast:
4	chr11:73108125..73109884-chr11:73115206..73117762,2	K562	blood:
5	chr11:73099755..73102272-chr11:73109128..73112969,3	K562	blood:

Variant related genes	Relation type
ENSG00000256928	TF binding region
ENSG00000054967	Chromatin interaction
ENSG00000256448	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1002126	0.88[CEU][hapmap]
rs10047442	1.00[CEU][hapmap];0.85[JPT][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10793060	1.00[CEU][hapmap];0.85[JPT][hapmap];0.87[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10898920	1.00[CEU][hapmap];0.85[JPT][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10898925	0.83[CEU][hapmap];0.85[JPT][hapmap];0.88[YRI][hapmap]
rs11235729	0.90[EUR][1000 genomes]
rs11235743	1.00[CEU][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11235746	1.00[CEU][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs11820786	0.81[EUR][1000 genomes]
rs11820929	0.84[CEU][hapmap]
rs11823923	0.84[CEU][hapmap]
rs11824614	0.83[CEU][hapmap]
rs11826896	0.83[CEU][hapmap];0.88[YRI][hapmap]
rs11826909	0.83[CEU][hapmap];0.92[YRI][hapmap]
rs12276536	0.81[EUR][1000 genomes]
rs12282282	0.83[CEU][hapmap]
rs12295744	1.00[CEU][hapmap];0.85[JPT][hapmap];0.85[YRI][hapmap]
rs12421053	0.94[CEU][hapmap];0.85[JPT][hapmap]
rs1939382	1.00[CEU][hapmap];0.85[JPT][hapmap];0.87[YRI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2298807	0.84[CEU][hapmap]
rs2366780	1.00[CEU][hapmap];0.82[JPT][hapmap];0.87[YRI][hapmap];0.83[EUR][1000 genomes]
rs3741148	1.00[CEU][hapmap];0.85[JPT][hapmap];0.88[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs55751428	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs56801796	0.89[EUR][1000 genomes]
rs6592521	0.84[CEU][hapmap]
rs7101831	0.84[CEU][hapmap];0.89[YRI][hapmap]
rs7114009	0.84[YRI][hapmap];0.80[AFR][1000 genomes]
rs7119167	0.94[CEU][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7122560	0.90[EUR][1000 genomes]
rs7127171	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7131383	0.83[CEU][hapmap]
rs73542998	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7925573	1.00[CEU][hapmap];0.85[JPT][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7935204	1.00[CEU][hapmap];0.85[JPT][hapmap];0.88[YRI][hapmap];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7937066	0.93[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs7945596	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7948630	1.00[CEU][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap]
rs7950002	1.00[CEU][hapmap];0.85[JPT][hapmap];0.81[EUR][1000 genomes]
rs7952686	1.00[CEU][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs876480	0.83[CEU][hapmap]
rs880317	1.00[CEU][hapmap];0.87[YRI][hapmap];0.93[AFR][1000 genomes];0.97[EUR][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	esv1821041	chr11:72937162-73113080	Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
2	esv3395161	chr11:73084616-73461577	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:73095200-73116200	Weak transcription	Liver	Liver
2	chr11:73096200-73130200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr11:73097200-73117600	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr11:73097400-73113000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr11:73097600-73110200	Weak transcription	NHDF-Ad	bronchial
6	chr11:73098600-73126000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr11:73098600-73132400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr11:73098800-73113000	Weak transcription	Fetal Brain Female	brain
9	chr11:73099200-73112400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr11:73099200-73139800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr11:73099200-73141000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr11:73099400-73112400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr11:73099400-73113200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr11:73099600-73119200	Weak transcription	Fetal Lung	lung
15	chr11:73100000-73116600	Weak transcription	Pancreas	Pancrea
16	chr11:73100000-73118400	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr11:73100200-73117400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr11:73100600-73118600	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr11:73100800-73115800	Weak transcription	HMEC	breast
20	chr11:73101000-73116200	Weak transcription	Brain Angular Gyrus	brain
21	chr11:73101000-73116400	Weak transcription	Brain Substantia Nigra	brain
22	chr11:73101200-73124800	Weak transcription	Psoas Muscle	Psoas
23	chr11:73101400-73110400	Strong transcription	GM12878-XiMat	blood
24	chr11:73101400-73112600	Weak transcription	HSMMtube	muscle
25	chr11:73101800-73110000	Strong transcription	Thymus	Thymus
26	chr11:73101800-73110200	Strong transcription	Dnd41	blood
27	chr11:73103600-73118400	Weak transcription	Esophagus	oesophagus
28	chr11:73103800-73116600	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr11:73104000-73116200	Weak transcription	Brain Anterior Caudate	brain
30	chr11:73104400-73111000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr11:73104600-73110000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr11:73104600-73110000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr11:73104600-73110400	Strong transcription	NHEK	skin
34	chr11:73104600-73112600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
35	chr11:73104600-73113200	Strong transcription	Primary monocytes fromperipheralblood	blood
36	chr11:73104600-73113200	Strong transcription	Monocytes-CD14+_RO01746	blood
37	chr11:73104600-73114400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr11:73104600-73123400	Strong transcription	Fetal Stomach	stomach
39	chr11:73104800-73110000	Weak transcription	NH-A	brain
40	chr11:73104800-73110200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr11:73104800-73112800	Weak transcription	Brain Germinal Matrix	brain
42	chr11:73104800-73114000	Strong transcription	Primary neutrophils fromperipheralblood	blood
43	chr11:73104800-73122600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr11:73105000-73110000	Weak transcription	K562	blood
45	chr11:73105200-73116400	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr11:73105200-73116800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr11:73105600-73116000	Weak transcription	Colonic Mucosa	Colon
48	chr11:73105800-73116600	Weak transcription	Primary T helper cells fromperipheralblood	blood
49	chr11:73106000-73114600	Weak transcription	HepG2	liver
50	chr11:73106200-73116400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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