Variant report

Variant	rs7857466
Chromosome Location	chr9:26891764-26891765
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:41)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:41 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MYC	chr9:26891502-26893054	MCF10A-Er-Src	breast:	n/a	chr9:26892866-26892876
2	CHD1	chr9:26891432-26893429	H1-hESC	embryonic stem cell:	n/a	n/a
3	TBP	chr9:26890977-26893272	Hela-S3	cervix:	n/a	n/a
4	CREB1	chr9:26891666-26893298	GM12878	blood:	n/a	n/a
5	POLR2A	chr9:26891697-26893623	Raji	blood:	n/a	n/a
6	UBTF	chr9:26891646-26893102	K562	blood:	n/a	n/a
7	POLR2A	chr9:26891461-26893661	GM19099	blood:	n/a	n/a
8	POLR2A	chr9:26891588-26893359	HepG2	liver:	n/a	n/a
9	POLR2A	chr9:26891741-26891811	K562	blood:	n/a	n/a
10	POLR2A	chr9:26891662-26893570	GM18505	blood:	n/a	n/a
11	BRCA1	chr9:26891346-26891824	Hela-S3	cervix:	n/a	n/a
12	GATA1	chr9:26891072-26893052	PBDE	blood:	n/a	n/a
13	RELA	chr9:26891690-26893092	GM15510	blood:	n/a	n/a
14	POLR2A	chr9:26891212-26893831	MCF10A-Er-Src	breast:	n/a	n/a
15	POLR2A	chr9:26890917-26893711	K562	blood:	n/a	n/a
16	IRF1	chr9:26891671-26893315	K562	blood:	n/a	n/a
17	POLR2A	chr9:26891580-26893690	K562	blood:	n/a	n/a
18	MYC	chr9:26891617-26891978	MCF10A-Er-Src	breast:	n/a	n/a
19	MYC	chr9:26891584-26893217	A549	lung:	n/a	chr9:26892866-26892876
20	TBL1XR1	chr9:26891049-26893676	K562	blood:	n/a	n/a
21	MAX	chr9:26891541-26893243	Hela-S3	cervix:	n/a	chr9:26892866-26892876
22	TCF7L2	chr9:26891591-26893018	Hela-S3	cervix:	n/a	n/a
23	POLR2A	chr9:26891475-26893753	H1-hESC	embryonic stem cell:	n/a	n/a
24	E2F4	chr9:26891490-26891856	MCF10A-Er-Src	breast:	n/a	n/a
25	POLR2A	chr9:26891084-26893746	MCF10A-Er-Src	breast:	n/a	n/a
26	POLR2A	chr9:26891476-26891948	GM12878	blood:	n/a	n/a
27	HCFC1	chr9:26891245-26893651	Hela-S3	cervix:	n/a	n/a
28	TCF7L2	chr9:26891624-26892111	Hela-S3	cervix:	n/a	n/a
29	POLR2A	chr9:26891262-26893632	IMR90	lung:	n/a	n/a
30	ZMIZ1	chr9:26891737-26893119	K562	blood:	n/a	n/a
31	KAP1	chr9:26891492-26893419	HEK293	kidney:	n/a	n/a
32	POLR2A	chr9:26891608-26893599	Hela-S3	cervix:	n/a	n/a
33	POLR2A	chr9:26891406-26893775	GM12891	blood:	n/a	n/a
34	CTCF	chr9:26891653-26892983	K562	blood:	n/a	n/a
35	POLR2A	chr9:26891503-26893712	GM12878	blood:	n/a	n/a
36	POLR2A	chr9:26891564-26893564	HepG2	liver:	n/a	n/a
37	POLR2A	chr9:26891463-26893612	Hela-S3	cervix:	n/a	n/a
38	MXI1	chr9:26891623-26893011	Hela-S3	cervix:	n/a	n/a
39	ARID3A	chr9:26891400-26891881	HepG2	liver:	n/a	n/a
40	MXI1	chr9:26890843-26893800	SK-N-SH	brain:	n/a	n/a
41	TBL1XR1	chr9:26891748-26893381	GM12878	blood:	n/a	n/a

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:26890555..26892142-chr9:26919709..26921210,2	MCF-7	breast:
2	chr9:26891080..26895841-chr9:26945501..26948974,8	K562	blood:
3	chr9:26891080..26894676-chr9:26945695..26949113,9	K562	blood:
4	chr9:26886338..26888156-chr9:26890310..26892766,2	MCF-7	breast:
5	chr9:26891289..26894164-chr9:26921199..26924471,3	MCF-7	breast:
6	chr9:26890425..26894629-chr9:26953159..26958312,6	K562	blood:
7	chr9:26890972..26893985-chr9:26945405..26948624,3	MCF-7	breast:
8	chr9:26886474..26888568-chr9:26890678..26892880,3	MCF-7	breast:
9	chr9:26890485..26893190-chr9:26945159..26948755,7	MCF-7	breast:
10	chr9:26889862..26894629-chr9:26953159..26958871,9	K562	blood:
11	chr9:26886311..26888299-chr9:26891061..26892871,2	K562	blood:

No data

Variant related genes	Relation type
RN7SL100P	TF binding region
CAAP1	TF binding region
ENSG00000137055	Chromatin interaction
ENSG00000096872	Chromatin interaction
ENSG00000120159	Chromatin interaction
ENSG00000234676	Chromatin interaction

Extended variants
information (count: 99 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:98)

rs_ID	r²[population]
rs1011358	0.80[ASN][1000 genomes]
rs10511796	0.86[CHB][hapmap]
rs10738762	0.80[JPT][hapmap]
rs10757635	0.80[CHB][hapmap];0.80[JPT][hapmap]
rs10812480	0.90[CHB][hapmap];0.85[JPT][hapmap]
rs10812485	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs10812490	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10812491	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10812494	1.00[CEU][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10812495	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10812502	0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10812505	0.81[CHB][hapmap]
rs10812506	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10812509	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs10812510	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs10812513	0.90[CHB][hapmap];0.85[JPT][hapmap]
rs10812517	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs10967545	0.93[EUR][1000 genomes]
rs10967560	0.90[CHB][hapmap]
rs10967566	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs10967575	0.90[ASN][1000 genomes]
rs10967581	1.00[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10967586	0.95[CHB][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs10967597	1.00[CEU][hapmap];0.95[JPT][hapmap];0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10967609	0.84[AMR][1000 genomes]
rs10967611	0.86[CHB][hapmap];0.87[AMR][1000 genomes]
rs10967612	0.85[AMR][1000 genomes]
rs10967614	0.87[AMR][1000 genomes]
rs10967621	0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10967622	0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10967623	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10967627	0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10967630	0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10967633	0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10967635	0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs10967636	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10967646	0.81[ASN][1000 genomes]
rs10967649	0.89[CHB][hapmap];0.95[JPT][hapmap]
rs10967650	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs10967661	0.90[CHB][hapmap]
rs10967678	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs10967681	0.95[CHB][hapmap];0.80[JPT][hapmap]
rs10967688	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs11534184	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11555693	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11562224	0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12235490	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12236404	0.87[AMR][1000 genomes]
rs12236850	0.89[CHB][hapmap]
rs12237867	0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12238035	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1336337	0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1414798	0.93[EUR][1000 genomes]
rs17760820	1.00[CEU][hapmap];0.85[CHB][hapmap];0.85[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17833941	1.00[CEU][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2184738	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3737226	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3739544	0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3739547	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3739548	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3739550	0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55827505	0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs55860736	0.87[AMR][1000 genomes]
rs55870543	0.87[AMR][1000 genomes]
rs57450012	0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs59159685	0.81[ASN][1000 genomes]
rs60841248	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6475945	0.81[JPT][hapmap]
rs7018943	0.90[CHB][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs7019034	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7019075	1.00[CEU][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7020010	0.85[JPT][hapmap]
rs7031903	0.85[AMR][1000 genomes]
rs7031984	0.86[CHB][hapmap];0.87[AMR][1000 genomes]
rs7034888	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7034899	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7035447	0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7038218	0.84[CHB][hapmap];0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs7042133	0.82[ASN][1000 genomes]
rs7042447	0.81[CHB][hapmap];0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs7045339	0.90[CHB][hapmap];0.80[JPT][hapmap];0.83[AMR][1000 genomes]
rs72703105	0.83[AMR][1000 genomes]
rs72719536	0.87[AMR][1000 genomes]
rs72719538	0.82[AMR][1000 genomes]
rs7849248	0.84[JPT][hapmap]
rs7856462	0.81[JPT][hapmap]
rs7857447	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs7857990	1.00[CEU][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7860542	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs7865952	0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7869798	0.85[CHB][hapmap]
rs7870787	0.85[JPT][hapmap]
rs7872496	0.90[CHB][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs7872666	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7873073	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7874940	0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7875171	0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs9644870	0.95[CHB][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1026827	chr9:26693515-26904699	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:26882800-26891800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr9:26882800-26892000	Weak transcription	Lung	lung
3	chr9:26883200-26892200	Weak transcription	Spleen	Spleen
4	chr9:26883400-26891800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr9:26883400-26892200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr9:26888200-26893600	Active TSS	K562	blood
7	chr9:26889600-26891800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr9:26890000-26893000	Active TSS	Hela-S3	cervix
9	chr9:26890200-26893400	Active TSS	Psoas Muscle	Psoas
10	chr9:26890200-26893600	Active TSS	HUES6 Cell Line	embryonic stem cell
11	chr9:26890400-26894400	Active TSS	ES-I3 Cell Line	embryonic stem cell
12	chr9:26890600-26892000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr9:26890600-26893000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr9:26890600-26893200	Active TSS	Fetal Intestine Large	intestine
15	chr9:26890600-26893200	Active TSS	A549	lung
16	chr9:26890600-26893600	Active TSS	Fetal Intestine Small	intestine
17	chr9:26890600-26893600	Active TSS	Rectal Mucosa Donor 29	rectum
18	chr9:26890800-26891800	Enhancers	Primary B cells from peripheral blood	blood
19	chr9:26890800-26892000	Weak transcription	Gastric	stomach
20	chr9:26890800-26892400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr9:26890800-26893000	Active TSS	Fetal Kidney	kidney
22	chr9:26890800-26893000	Active TSS	GM12878-XiMat	blood
23	chr9:26890800-26893200	Active TSS	HUES48 Cell Line	embryonic stem cell
24	chr9:26890800-26893200	Active TSS	Colonic Mucosa	Colon
25	chr9:26890800-26893200	Active TSS	Duodenum Mucosa	Duodenum
26	chr9:26890800-26893600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr9:26890800-26893600	Active TSS	HSMM	muscle
28	chr9:26891000-26891800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr9:26891000-26891800	Enhancers	Primary neutrophils fromperipheralblood	blood
30	chr9:26891000-26891800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
31	chr9:26891000-26891800	Flanking Active TSS	Liver	Liver
32	chr9:26891000-26891800	Flanking Active TSS	HUVEC	blood vessel
33	chr9:26891000-26892000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr9:26891000-26892200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr9:26891000-26892400	Flanking Active TSS	Primary hematopoietic stem cells	blood
36	chr9:26891000-26893000	Active TSS	Muscle Satellite Cultured Cells	--
37	chr9:26891000-26893000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr9:26891000-26893200	Active TSS	Aorta	Aorta
39	chr9:26891000-26893200	Active TSS	Fetal Stomach	stomach
40	chr9:26891000-26893200	Active TSS	Right Ventricle	heart
41	chr9:26891000-26893200	Active TSS	Thymus	Thymus
42	chr9:26891000-26893200	Active TSS	HSMMtube	muscle
43	chr9:26891000-26893400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
44	chr9:26891000-26893400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr9:26891000-26893400	Active TSS	Right Atrium	heart
46	chr9:26891000-26893600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr9:26891200-26892200	Flanking Active TSS	Primary T cells from cord blood	blood
48	chr9:26891200-26892600	Active TSS	Skeletal Muscle Female	skeletal muscle
49	chr9:26891200-26893000	Active TSS	Primary hematopoietic stem cells short term culture	blood
50	chr9:26891200-26893000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain

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