Variant report

Variant	rs6828254
Chromosome Location	chr4:110737549-110737550
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	HA-E2F1	chr4:110736132-110737619	MCF-7	breast:	n/a	chr4:110736983-110736992
2	POLR2A	chr4:110736217-110737628	HL-60	blood:	n/a	n/a
3	MAX	chr4:110736161-110737605	HCT-116	colon:	n/a	chr4:110736945-110736955
4	MAX	chr4:110736215-110737646	K562	blood:	n/a	chr4:110736945-110736955
5	TCF7L2	chr4:110736379-110737619	HCT-116	colon:	n/a	n/a
6	POLR2A	chr4:110736193-110737585	GM12892	blood:	n/a	n/a
7	MXI1	chr4:110736098-110737663	GM12878	blood:	n/a	n/a
8	MYC	chr4:110736400-110737698	MCF10A-Er-Src	breast:	n/a	chr4:110736945-110736955
9	CHD2	chr4:110736185-110737646	GM12878	blood:	n/a	n/a
10	MXI1	chr4:110736197-110737667	HepG2	liver:	n/a	n/a
11	MYC	chr4:110736280-110737850	K562	blood:	n/a	chr4:110736945-110736955
12	POLR2A	chr4:110736290-110737629	Hela-S3	cervix:	n/a	n/a
13	POLR2A	chr4:110736191-110737592	K562	blood:	n/a	n/a
14	SMC3	chr4:110737502-110737673	K562	blood:	n/a	n/a
15	POLR2A	chr4:110736070-110737761	MCF10A-Er-Src	breast:	n/a	n/a
16	POLR2A	chr4:110736168-110737727	H1-hESC	embryonic stem cell:	n/a	n/a
17	RUNX3	chr4:110736150-110737578	GM12878	blood:	n/a	n/a
18	MXI1	chr4:110735827-110739409	SK-N-SH	brain:	n/a	n/a
19	EGR1	chr4:110737253-110737637	K562	blood:	n/a	chr4:110737362-110737376 chr4:110737416-110737430
20	MAX	chr4:110736252-110737628	SK-N-SH	brain:	n/a	chr4:110736945-110736955
21	SIN3AK20	chr4:110736124-110737587	K562	blood:	n/a	n/a
22	POLR2A	chr4:110736149-110737787	SK-N-MC	brain:	n/a	n/a
23	MAZ	chr4:110736027-110737584	IMR90	lung:	n/a	n/a
24	MAX	chr4:110736438-110737589	Hela-S3	cervix:	n/a	chr4:110736945-110736955
25	NR2F2	chr4:110735701-110737852	K562	blood:	n/a	n/a
26	MAX	chr4:110736292-110737598	NB4	blood:	n/a	chr4:110736945-110736955
27	SIN3A	chr4:110736099-110737555	GM12878	blood:	n/a	chr4:110737131-110737141
28	POLR2A	chr4:110736290-110737677	IMR90	lung:	n/a	n/a
29	POLR2A	chr4:110736016-110738028	K562	blood:	n/a	n/a
30	REST	chr4:110736059-110737699	H1-neurons	neurons:	n/a	chr4:110737131-110737140
31	SIN3A	chr4:110735973-110737710	H1-hESC	embryonic stem cell:	n/a	chr4:110737131-110737141
32	POLR2A	chr4:110736136-110737659	HL-60	blood:	n/a	n/a
33	MYC	chr4:110736305-110737663	MCF10A-Er-Src	breast:	n/a	chr4:110736945-110736955
34	POLR2A	chr4:110736257-110737551	GM12892	blood:	n/a	n/a
35	MXI1	chr4:110736313-110737700	K562	blood:	n/a	n/a
36	UBTF	chr4:110737354-110737554	K562	blood:	n/a	n/a
37	GABPA	chr4:110736176-110737549	SK-N-SH	brain:	n/a	n/a
38	POLR2A	chr4:110736191-110737714	GM12878	blood:	n/a	n/a
39	POLR2A	chr4:110736094-110737725	GM12891	blood:	n/a	n/a
40	POLR2A	chr4:110737486-110737585	MCF-7	breast:	n/a	n/a
41	E2F4	chr4:110736400-110737563	MCF10A-Er-Src	breast:	n/a	chr4:110736983-110736992
42	POLR2A	chr4:110736261-110737557	GM18505	blood:	n/a	n/a
43	MYC	chr4:110735905-110737851	K562	blood:	n/a	chr4:110736945-110736955
44	MXI1	chr4:110735986-110737847	IMR90	lung:	n/a	n/a
45	IRF1	chr4:110737508-110738654	K562	blood:	n/a	chr4:110738173-110738186 chr4:110738172-110738186 chr4:110738175-110738185 chr4:110738173-110738186 chr4:110738173-110738187 chr4:110738173-110738186 chr4:110738171-110738185 chr4:110738175-110738186 chr4:110738175-110738189 chr4:110738174-110738188 chr4:110738174-110738191 chr4:110738180-110738187
46	CREB1	chr4:110736111-110737672	K562	blood:	n/a	n/a
47	POLR2A	chr4:110736075-110737700	K562	blood:	n/a	n/a
48	POLR2A	chr4:110737479-110737624	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:110721548..110724346-chr4:110736767..110738481,2	MCF-7	breast:
2	chr4:110622109..110625008-chr4:110733953..110738254,7	MCF-7	breast:
3	chr4:110648642..110653205-chr4:110733223..110738599,11	K562	blood:
4	chr4:109570584..109572425-chr4:110736914..110740419,3	K562	blood:
5	chr4:110736448..110738364-chr4:110748018..110749742,2	MCF-7	breast:
6	chr4:110733962..110737774-chr4:110769396..110773000,3	K562	blood:
7	chr4:110353826..110356085-chr4:110735938..110738635,3	MCF-7	breast:
8	chr4:110648895..110652104-chr4:110733858..110738186,8	K562	blood:
9	chr4:110622297..110625771-chr4:110735143..110738902,5	K562	blood:
10	chr4:110736083..110738603-chr4:110880229..110882607,2	K562	blood:
11	chr4:110736207..110737987-chr4:111118065..111119970,2	K562	blood:
12	chr13:31038798..31040752-chr4:110734724..110737666,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000272795	TF binding region
ENSG00000138802	Chromatin interaction
ENSG00000123739	Chromatin interaction
ENSG00000189403	Chromatin interaction
ENSG00000205403	Chromatin interaction
ENSG00000138794	Chromatin interaction
ENSG00000180245	Chromatin interaction
ENSG00000247950	Chromatin interaction
ENSG00000183423	Chromatin interaction
ENSG00000138798	Chromatin interaction
ENSG00000170522	Chromatin interaction
ENSG00000198856	Chromatin interaction

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

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

rs_ID	r²[population]
rs10004390	1.00[EUR][1000 genomes]
rs10007208	1.00[ASW][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs1007050	1.00[EUR][1000 genomes]
rs10488880	1.00[EUR][1000 genomes]
rs11568961	1.00[ASW][hapmap]
rs11569124	1.00[EUR][1000 genomes]
rs11569132	1.00[EUR][1000 genomes]
rs11936595	1.00[EUR][1000 genomes]
rs11940838	1.00[EUR][1000 genomes]
rs17040933	1.00[EUR][1000 genomes]
rs17041176	1.00[EUR][1000 genomes]
rs28361433	1.00[EUR][1000 genomes]
rs28437024	1.00[EUR][1000 genomes]
rs28682326	1.00[EUR][1000 genomes]
rs41464250	1.00[EUR][1000 genomes]
rs4698796	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56285361	1.00[EUR][1000 genomes]
rs56737575	1.00[EUR][1000 genomes]
rs6533467	1.00[MEX][hapmap];1.00[EUR][1000 genomes]
rs6533468	1.00[AMR][1000 genomes]
rs6811614	1.00[EUR][1000 genomes]
rs6829540	1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6832396	1.00[EUR][1000 genomes]
rs6854247	1.00[EUR][1000 genomes]
rs72892672	1.00[EUR][1000 genomes]
rs73839166	1.00[EUR][1000 genomes]
rs73841124	1.00[EUR][1000 genomes]
rs7681770	1.00[MEX][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9994891	1.00[MEX][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	nsv530156	chr4:110721397-110911297	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 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	chr4:110735400-110737600	Active TSS	K562	blood
2	chr4:110735800-110737600	Active TSS	iPS-15b Cell Line	embryonic stem cell
3	chr4:110735800-110737600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr4:110735800-110737600	Active TSS	Brain Anterior Caudate	brain
5	chr4:110735800-110737600	Active TSS	Fetal Intestine Small	intestine
6	chr4:110735800-110737600	Active TSS	Fetal Kidney	kidney
7	chr4:110735800-110737600	Active TSS	Pancreatic Islets	Pancreatic Islet
8	chr4:110735800-110737600	Active TSS	Fetal Lung	lung
9	chr4:110735800-110737800	Active TSS	H1 Cell Line	embryonic stem cell
10	chr4:110735800-110737800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr4:110735800-110737800	Active TSS	iPS-18 Cell Line	embryonic stem cell
12	chr4:110735800-110737800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr4:110735800-110737800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr4:110735800-110737800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr4:110735800-110738000	Active TSS	ES-I3 Cell Line	embryonic stem cell
16	chr4:110735800-110738000	Active TSS	HMEC	breast
17	chr4:110735800-110738400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr4:110735800-110738400	Active TSS	HUES6 Cell Line	embryonic stem cell
19	chr4:110735800-110738400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr4:110735800-110738600	Active TSS	HUES48 Cell Line	embryonic stem cell
21	chr4:110735800-110738600	Active TSS	HUES64 Cell Line	embryonic stem cell
22	chr4:110736000-110737600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
23	chr4:110736000-110737600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr4:110736000-110737600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr4:110736000-110737600	Active TSS	Muscle Satellite Cultured Cells	--
26	chr4:110736000-110737600	Active TSS	Aorta	Aorta
27	chr4:110736000-110737600	Active TSS	Fetal Stomach	stomach
28	chr4:110736000-110737600	Active TSS	Rectal Smooth Muscle	rectum
29	chr4:110736000-110737600	Active TSS	Right Ventricle	heart
30	chr4:110736000-110737800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr4:110736000-110737800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr4:110736000-110737800	Active TSS	Left Ventricle	heart
33	chr4:110736000-110737800	Active TSS	Stomach Mucosa	stomach
34	chr4:110736000-110737800	Active TSS	NHLF	lung
35	chr4:110736000-110738000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr4:110736000-110738000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr4:110736000-110738000	Active TSS	Brain Cingulate Gyrus	brain
38	chr4:110736000-110738000	Active TSS	A549	lung
39	chr4:110736000-110738000	Active TSS	NHDF-Ad	bronchial
40	chr4:110736000-110738200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr4:110736000-110738200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr4:110736000-110738400	Active TSS	H9 Cell Line	embryonic stem cell
43	chr4:110736000-110738400	Active TSS	Psoas Muscle	Psoas
44	chr4:110736000-110738600	Active TSS	iPS-20b Cell Line	embryonic stem cell
45	chr4:110736000-110739200	Active TSS	GM12878-XiMat	blood
46	chr4:110736200-110737600	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr4:110736200-110737600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr4:110736200-110737600	Active TSS	Primary T killer memory cells from peripheral blood	blood
49	chr4:110736200-110737600	Active TSS	Duodenum Smooth Muscle	Duodenum
50	chr4:110736200-110737600	Active TSS	Fetal Heart	heart

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