Variant report

Variant	rs6953596
Chromosome Location	chr7:25989298-25989299
allele	A/C
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	SIN3A	chr7:25989265-25991735	H1-hESC	embryonic stem cell:	n/a	chr7:25990195-25990206 chr7:25990193-25990206 chr7:25991169-25991182 chr7:25990724-25990737 chr7:25991166-25991175 chr7:25991177-25991190 chr7:25990883-25990894
2	POLR2A	chr7:25985526-25991809	GM19099	blood:	n/a	n/a
3	HEY1	chr7:25989259-25989743	HepG2	liver:	n/a	n/a
4	MAX	chr7:25989212-25989717	HepG2	liver:	n/a	n/a
5	TBP	chr7:25989276-25989927	K562	blood:	n/a	n/a
6	MBD4	chr7:25989079-25989701	HepG2	liver:	n/a	n/a
7	POLR2A	chr7:25987021-25992694	HepG2	liver:	n/a	n/a
8	POLR2A	chr7:25986974-25991365	HepG2	liver:	n/a	n/a
9	CREB1	chr7:25989239-25991492	HepG2	liver:	n/a	n/a
10	JUND	chr7:25989286-25989739	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr7:25989248-25989702	HepG2	liver:	n/a	n/a
12	POLR2A	chr7:25986274-25991748	GM18526	blood:	n/a	n/a
13	POLR2A	chr7:25989232-25989798	HepG2	liver:	n/a	n/a
14	POLR2A	chr7:25989121-25989633	K562	blood:	n/a	n/a
15	MAX	chr7:25989202-25990609	H1-hESC	embryonic stem cell:	n/a	n/a
16	MAX	chr7:25989274-25989657	K562	blood:	n/a	n/a
17	POLR2A	chr7:25985030-25991406	GM12878	blood:	n/a	n/a
18	MAZ	chr7:25989269-25991382	K562	blood:	n/a	chr7:25990932-25990943 chr7:25991249-25991259
19	E2F6	chr7:25989145-25989792	H1-hESC	embryonic stem cell:	n/a	chr7:25989460-25989467
20	POLR2A	chr7:25989181-25991421	GM19193	blood:	n/a	n/a
21	CEBPB	chr7:25989186-25989386	K562	blood:	n/a	n/a
22	PML	chr7:25989241-25989809	K562	blood:	n/a	n/a
23	RUNX3	chr7:25989276-25989994	GM12878	blood:	n/a	n/a
24	MYC	chr7:25989214-25989752	K562	blood:	n/a	n/a
25	MTA3	chr7:25989263-25989945	GM12878	blood:	n/a	n/a
26	MAX	chr7:25989203-25989699	K562	blood:	n/a	n/a
27	TEAD4	chr7:25989205-25989961	K562	blood:	n/a	n/a
28	MAX	chr7:25989127-25989757	HepG2	liver:	n/a	n/a
29	RCOR1	chr7:25989255-25991064	K562	blood:	n/a	n/a
30	POLR2A	chr7:25988968-25989832	HepG2	liver:	n/a	n/a
31	ATF2	chr7:25989256-25989966	H1-hESC	embryonic stem cell:	n/a	n/a
32	MXI1	chr7:25988971-25990128	GM12878	blood:	n/a	n/a
33	POLR2A	chr7:25989156-25991518	H1-hESC	embryonic stem cell:	n/a	n/a
34	POLR2A	chr7:25989186-25991998	H1-hESC	embryonic stem cell:	n/a	n/a
35	MYC	chr7:25989173-25989551	H1-hESC	embryonic stem cell:	n/a	n/a
36	JUN	chr7:25989081-25991424	K562	blood:	n/a	chr7:25990816-25990825 chr7:25990830-25990839 chr7:25991100-25991109
37	POLR2A	chr7:25989122-25991741	GM18951	blood:	n/a	n/a
38	MAX	chr7:25989295-25991413	NB4	blood:	n/a	chr7:25990932-25990943 chr7:25991249-25991259
39	TAF1	chr7:25989283-25989732	H1-hESC	embryonic stem cell:	n/a	n/a
40	MXI1	chr7:25989217-25989607	H1-hESC	embryonic stem cell:	n/a	n/a
41	POLR2A	chr7:25989185-25990074	GM12878	blood:	n/a	n/a
42	MAX	chr7:25989187-25989603	H1-hESC	embryonic stem cell:	n/a	n/a
43	MAX	chr7:25989212-25989684	H1-hESC	embryonic stem cell:	n/a	n/a
44	POLR2A	chr7:25985198-25990343	GM12891	blood:	n/a	n/a
45	TBP	chr7:25989281-25989637	HepG2	liver:	n/a	n/a
46	POLR2A	chr7:25984487-25990939	K562	blood:	n/a	n/a
47	SMC3	chr7:25989110-25989898	GM12878	blood:	n/a	chr7:25989477-25989484
48	MYBL2	chr7:25989190-25989750	HepG2	liver:	n/a	n/a
49	POLR2A	chr7:25989126-25991397	GM15510	blood:	n/a	n/a
50	POLR2A	chr7:25989211-25990998	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:25989265..25991851-chr7:26238825..26240746,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000270933	TF binding region
ENSG00000122566	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10261878	0.82[AMR][1000 genomes]
rs13231897	0.86[AFR][1000 genomes]
rs4412274	0.81[AFR][1000 genomes]
rs62446277	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6461895	0.86[EUR][1000 genomes]
rs6461897	0.86[EUR][1000 genomes]
rs66892818	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs67612070	0.86[EUR][1000 genomes]
rs6947509	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6966574	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6977848	0.87[AFR][1000 genomes]
rs7787943	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7810027	0.86[EUR][1000 genomes]

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	nsv1016813	chr7:25405859-26150509	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	108 gene(s)	inside rSNPs	diseases
2	nsv538803	chr7:25405859-26150509	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	108 gene(s)	inside rSNPs	diseases
3	nsv606432	chr7:25988185-26223294	Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	102 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:25980800-25989400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr7:25985600-25989400	Weak transcription	Esophagus	oesophagus
3	chr7:25985600-25989400	Weak transcription	Gastric	stomach
4	chr7:25986000-25989400	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr7:25987200-25993200	Active TSS	Pancreas	Pancrea
6	chr7:25987800-25989400	Enhancers	H9 Cell Line	embryonic stem cell
7	chr7:25987800-25992800	Active TSS	Pancreatic Islets	Pancreatic Islet
8	chr7:25988000-25989600	Weak transcription	Right Atrium	heart
9	chr7:25988200-25989400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr7:25988200-25989400	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
11	chr7:25988200-25990000	Flanking Active TSS	Liver	Liver
12	chr7:25988200-25990200	Flanking Active TSS	Duodenum Mucosa	Duodenum
13	chr7:25988400-25989400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
14	chr7:25988400-25989400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr7:25988400-25989400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
16	chr7:25988400-25989400	Enhancers	Stomach Mucosa	stomach
17	chr7:25988400-25990200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr7:25988600-25989400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr7:25988600-25989400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
20	chr7:25988600-25989400	Bivalent Enhancer	Fetal Muscle Leg	muscle
21	chr7:25988600-25989600	Enhancers	Primary T helper cells fromperipheralblood	blood
22	chr7:25988600-25989600	Enhancers	Lung	lung
23	chr7:25988800-25989400	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr7:25988800-25989400	Enhancers	Adipose Nuclei	Adipose
25	chr7:25988800-25989400	Active TSS	Duodenum Smooth Muscle	Duodenum
26	chr7:25988800-25989600	Enhancers	Primary T cells fromperipheralblood	blood
27	chr7:25988800-25989600	Enhancers	Primary T helper cells PMA-I stimulated	--
28	chr7:25988800-25989600	Enhancers	Primary T killer memory cells from peripheral blood	blood
29	chr7:25988800-25989600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr7:25988800-25989800	Flanking Active TSS	Thymus	Thymus
31	chr7:25989000-25989400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr7:25989000-25989400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr7:25989000-25989400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
34	chr7:25989000-25989400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr7:25989000-25989400	Enhancers	Primary hematopoietic stem cells short term culture	blood
36	chr7:25989000-25989400	Active TSS	Fetal Intestine Small	intestine
37	chr7:25989000-25989600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
38	chr7:25989000-25989600	Bivalent Enhancer	Primary B cells from peripheral blood	blood
39	chr7:25989000-25989600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
40	chr7:25989000-25989600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
41	chr7:25989000-25989600	Enhancers	Small Intestine	intestine
42	chr7:25989000-25990000	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
43	chr7:25989000-25990000	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
44	chr7:25989000-25990000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr7:25989000-25990000	Flanking Active TSS	K562	blood
46	chr7:25989000-25990200	Flanking Active TSS	Fetal Thymus	thymus
47	chr7:25989000-25990200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
48	chr7:25989000-25991400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr7:25989200-25989400	Active TSS	H1 Cell Line	embryonic stem cell
50	chr7:25989200-25989400	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell

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