Variant report

Variant	rs28478192
Chromosome Location	chr4:99181521-99181522
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	YY1	chr4:99181166-99182447	K562	blood:	n/a	chr4:99181333-99181345 chr4:99181337-99181345 chr4:99181940-99181951
2	UBTF	chr4:99181187-99183389	K562	blood:	n/a	n/a
3	TCF7L2	chr4:99181379-99181948	MCF-7	breast:	n/a	chr4:99181622-99181636 chr4:99181622-99181638 chr4:99181626-99181635 chr4:99181622-99181638 chr4:99181624-99181634
4	ZNF263	chr4:99181254-99182338	HEK293-T-REx	kidney:	n/a	n/a
5	POLR2A	chr4:99180313-99182895	SK-N-MC	brain:	n/a	n/a
6	CHD1	chr4:99181073-99182184	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr4:99181304-99182754	HepG2	liver:	n/a	n/a
8	POLR2A	chr4:99181300-99182443	K562	blood:	n/a	n/a
9	POLR2A	chr4:99181141-99182918	HCT-116	colon:	n/a	n/a
10	POLR2A	chr4:99181297-99183179	MCF-7	breast:	n/a	n/a
11	POLR2A	chr4:99180509-99182731	K562	blood:	n/a	n/a
12	TAF7	chr4:99181330-99182487	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr4:99180576-99183393	K562	blood:	n/a	n/a
14	POLR2A	chr4:99181259-99183246	K562	blood:	n/a	n/a
15	RCOR1	chr4:99181278-99182391	HepG2	liver:	n/a	n/a
16	MAFK	chr4:99181172-99182251	Hela-S3	cervix:	n/a	chr4:99181225-99181240 chr4:99181226-99181237
17	SMARCC1	chr4:99181085-99182253	Hela-S3	cervix:	n/a	n/a
18	TBP	chr4:99181097-99182488	HepG2	liver:	n/a	n/a
19	BHLHE40	chr4:99181174-99182504	GM12878	blood:	n/a	chr4:99182283-99182299
20	CHD2	chr4:99181407-99183476	Hela-S3	cervix:	n/a	n/a
21	HEY1	chr4:99181329-99181647	K562	blood:	n/a	n/a
22	YY1	chr4:99181240-99183230	HepG2	liver:	n/a	chr4:99181333-99181345 chr4:99182550-99182564 chr4:99181337-99181345 chr4:99182552-99182561 chr4:99181940-99181951
23	POLR2A	chr4:99180639-99183583	Raji	blood:	n/a	n/a
24	MAX	chr4:99181310-99182506	ECC-1	luminal epithelium:	n/a	chr4:99181518-99181528 chr4:99182388-99182398
25	POLR2A	chr4:99181272-99181733	H1-hESC	embryonic stem cell:	n/a	n/a
26	POLR2A	chr4:99180532-99183540	MCF10A-Er-Src	breast:	n/a	n/a
27	YY1	chr4:99181178-99181744	GM12892	blood:	n/a	chr4:99181333-99181345 chr4:99181337-99181345
28	ZNF143	chr4:99181337-99183327	GM12878	blood:	n/a	chr4:99181609-99181619 chr4:99182886-99182904 chr4:99182890-99182900 chr4:99182487-99182497 chr4:99181515-99181525 chr4:99181636-99181646
29	YY1	chr4:99181224-99182714	SK-N-SH	brain:	n/a	chr4:99181333-99181345 chr4:99182550-99182564 chr4:99181337-99181345 chr4:99182552-99182561 chr4:99181940-99181951
30	MAX	chr4:99181114-99183611	HCT-116	colon:	n/a	chr4:99181518-99181528 chr4:99182388-99182398
31	MAZ	chr4:99181310-99183517	K562	blood:	n/a	chr4:99181518-99181528 chr4:99182388-99182398
32	POLR2A	chr4:99181311-99182987	K562	blood:	n/a	n/a
33	MXI1	chr4:99181314-99181580	GM12878	blood:	n/a	n/a
34	MAX	chr4:99181167-99183535	H1-hESC	embryonic stem cell:	n/a	chr4:99181518-99181528 chr4:99182388-99182398
35	TAF1	chr4:99181353-99182797	H1-hESC	embryonic stem cell:	n/a	n/a
36	TAF1	chr4:99181414-99181695	SK-N-SH	brain:	n/a	n/a
37	POLR2A	chr4:99180609-99182928	GM12878	blood:	n/a	n/a
38	TCF7L2	chr4:99181062-99182044	HEK293	kidney:	n/a	chr4:99181622-99181636 chr4:99181622-99181638 chr4:99181626-99181635 chr4:99181622-99181638 chr4:99181624-99181634
39	MAX	chr4:99181288-99183565	ECC-1	luminal epithelium:	n/a	chr4:99181518-99181528 chr4:99182388-99182398
40	MTA3	chr4:99181435-99182263	GM12878	blood:	n/a	n/a
41	BHLHE40	chr4:99181212-99182502	HepG2	liver:	n/a	chr4:99182283-99182299
42	POLR2A	chr4:99180827-99183493	GM18505	blood:	n/a	n/a
43	MAX	chr4:99181374-99183520	Hela-S3	cervix:	n/a	chr4:99181518-99181528 chr4:99182388-99182398
44	POLR2A	chr4:99181256-99182454	HCT-116	colon:	n/a	n/a
45	POLR2A	chr4:99181228-99182470	HepG2	liver:	n/a	n/a
46	CHD1	chr4:99181240-99182789	GM12878	blood:	n/a	n/a
47	POLR2A	chr4:99180574-99182916	HepG2	liver:	n/a	n/a
48	POLR2A	chr4:99181334-99183220	GM18951	blood:	n/a	n/a
49	SIN3AK20	chr4:99181107-99183524	MCF-7	breast:	n/a	n/a
50	USF2	chr4:99181390-99181617	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:99063087..99065504-chr4:99179455..99182247,2	MCF-7	breast:
2	chr4:99086672..99088660-chr4:99180652..99182426,2	MCF-7	breast:
3	chr4:99180773..99182396-chr4:99197532..99199081,2	K562	blood:
4	chr4:99181413..99182409-chr6:43737724..43738351,2	Hela-S3	cervix:
5	chr4:99180005..99182414-chr4:99204613..99206874,2	K562	blood:
6	chr4:99166826..99169265-chr4:99180288..99182314,2	MCF-7	breast:
7	chr4:99062262..99068404-chr4:99178848..99183768,9	MCF-7	breast:
8	chr20:55925000..55927785-chr4:99180687..99182199,2	MCF-7	breast:
9	chr4:99177008..99180462-chr4:99180782..99182422,3	K562	blood:
10	chr4:99076051..99077551-chr4:99180191..99182364,2	MCF-7	breast:
11	chr4:99180743..99183219-chr4:99577927..99581407,3	MCF-7	breast:

Variant related genes	Relation type
RAP1GDS1	TF binding region
ENSG00000163116	Chromatin interaction
ENSG00000101146	Chromatin interaction
ENSG00000112715	Chromatin interaction
ENSG00000168785	Chromatin interaction
ENSG00000260641	Chromatin interaction

Extended variants
information (count: 97 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs10001137	1.00[AMR][1000 genomes]
rs10003061	1.00[AMR][1000 genomes]
rs10003496	1.00[ASW][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10006734	1.00[AMR][1000 genomes]
rs10010260	1.00[AMR][1000 genomes]
rs10013248	1.00[ASW][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes]
rs10015953	1.00[AMR][1000 genomes]
rs10017075	1.00[AMR][1000 genomes]
rs10017827	1.00[AMR][1000 genomes]
rs10022073	1.00[AMR][1000 genomes]
rs10025311	1.00[AMR][1000 genomes]
rs10026222	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10027925	1.00[AMR][1000 genomes]
rs10029895	1.00[ASW][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes]
rs10032785	0.91[AMR][1000 genomes]
rs10034649	1.00[AMR][1000 genomes]
rs10050289	0.83[AMR][1000 genomes]
rs10212883	1.00[AMR][1000 genomes]
rs1024127	1.00[GIH][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes]
rs10470953	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12331722	0.91[AMR][1000 genomes]
rs12509125	1.00[TSI][hapmap]
rs13353633	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16996571	0.91[AMR][1000 genomes]
rs17027388	0.80[AMR][1000 genomes]
rs17027393	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17027526	0.87[ASW][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes]
rs17027538	1.00[ASW][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes]
rs17027559	0.91[AMR][1000 genomes]
rs17027596	0.83[AMR][1000 genomes]
rs17027597	0.91[AMR][1000 genomes]
rs17027617	1.00[AMR][1000 genomes]
rs28374939	1.00[AMR][1000 genomes]
rs28407050	1.00[AMR][1000 genomes]
rs28438716	1.00[AMR][1000 genomes]
rs28446845	1.00[AMR][1000 genomes]
rs28451188	0.91[AMR][1000 genomes]
rs28455818	1.00[AMR][1000 genomes]
rs28459325	0.91[AMR][1000 genomes]
rs28464398	0.83[AMR][1000 genomes]
rs28472340	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28494643	1.00[AMR][1000 genomes]
rs28497963	0.91[AMR][1000 genomes]
rs28503871	0.83[AMR][1000 genomes]
rs28529663	1.00[AMR][1000 genomes]
rs28558542	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28564255	1.00[AMR][1000 genomes]
rs28589745	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28647503	1.00[AMR][1000 genomes]
rs28649922	1.00[AMR][1000 genomes]
rs28651612	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28664868	1.00[AMR][1000 genomes]
rs28705201	0.80[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs28731135	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28786730	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28806635	1.00[AMR][1000 genomes]
rs28807427	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28840158	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28882140	0.83[AMR][1000 genomes]
rs28883979	0.91[AMR][1000 genomes]
rs28893208	1.00[AMR][1000 genomes]
rs41275691	0.91[AMR][1000 genomes]
rs41275693	1.00[AMR][1000 genomes]
rs41525749	1.00[AMR][1000 genomes]
rs56805018	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59725407	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60544326	0.83[AMR][1000 genomes]
rs6831386	1.00[AMR][1000 genomes]
rs6834495	1.00[AMR][1000 genomes]
rs6858042	1.00[AMR][1000 genomes]
rs73834403	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73834404	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73834429	1.00[AMR][1000 genomes]
rs73834444	1.00[AMR][1000 genomes]
rs73834475	0.91[AMR][1000 genomes]
rs73834479	1.00[AMR][1000 genomes]
rs73834489	0.91[AMR][1000 genomes]
rs7655622	1.00[ASW][hapmap];1.00[GIH][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs7656868	1.00[AMR][1000 genomes]
rs7658383	1.00[ASW][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes]
rs9307226	0.91[AMR][1000 genomes]
rs9991668	1.00[ASW][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9994467	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9995184	1.00[GIH][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes]
rs9997337	1.00[GIH][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes]
rs9997973	0.83[AMR][1000 genomes]
rs9998801	0.91[AMR][1000 genomes]
rs9999779	1.00[GIH][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529623	chr4:98501338-99460166	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
2	nsv1001570	chr4:98976239-99239838	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv1004616	chr4:99085875-99308901	Genic enhancers Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	esv2763801	chr4:99094892-99413853	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	esv2754250	chr4:99094922-99527122	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers 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	20 gene(s)	inside rSNPs	diseases
6	nsv879651	chr4:99105055-99441349	Weak transcription Genic enhancers Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv879652	chr4:99125659-99303633	Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
8	nsv528127	chr4:99146436-99229839	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
9	nsv879653	chr4:99152631-99260423	Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 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	chr4:99180600-99181600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
2	chr4:99180600-99181600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr4:99180600-99181600	Flanking Active TSS	HMEC	breast
4	chr4:99180600-99181600	Flanking Active TSS	NHLF	lung
5	chr4:99180600-99181600	Flanking Active TSS	Osteobl	bone
6	chr4:99180600-99181800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr4:99180600-99181800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr4:99180600-99181800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
9	chr4:99180600-99182000	Flanking Active TSS	Primary T cells from cord blood	blood
10	chr4:99180600-99182000	Flanking Active TSS	Adipose Nuclei	Adipose
11	chr4:99180600-99182200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
12	chr4:99180600-99184000	Active TSS	HUES64 Cell Line	embryonic stem cell
13	chr4:99180800-99181600	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
14	chr4:99180800-99181600	Flanking Active TSS	Liver	Liver
15	chr4:99180800-99181600	Flanking Active TSS	Fetal Muscle Leg	muscle
16	chr4:99180800-99181600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
17	chr4:99180800-99181600	Flanking Active TSS	HUVEC	blood vessel
18	chr4:99180800-99181600	Flanking Active TSS	NHEK	skin
19	chr4:99180800-99181800	Flanking Active TSS	Primary B cells from cord blood	blood
20	chr4:99180800-99181800	Flanking Active TSS	Primary hematopoietic stem cells	blood
21	chr4:99180800-99181800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr4:99180800-99181800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
23	chr4:99180800-99182200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
24	chr4:99180800-99183400	Active TSS	Pancreatic Islets	Pancreatic Islet
25	chr4:99180800-99183600	Active TSS	Colonic Mucosa	Colon
26	chr4:99180800-99183800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr4:99180800-99183800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr4:99180800-99184000	Active TSS	Aorta	Aorta
29	chr4:99180800-99184200	Active TSS	HSMMtube	muscle
30	chr4:99181000-99181600	Flanking Active TSS	Brain Substantia Nigra	brain
31	chr4:99181000-99181600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
32	chr4:99181000-99181600	Flanking Active TSS	Fetal Thymus	thymus
33	chr4:99181000-99181800	Flanking Active TSS	Primary B cells from peripheral blood	blood
34	chr4:99181000-99181800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
35	chr4:99181000-99182000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr4:99181000-99182600	Active TSS	Brain Germinal Matrix	brain
37	chr4:99181000-99183000	Active TSS	ES-I3 Cell Line	embryonic stem cell
38	chr4:99181000-99183200	Active TSS	Rectal Mucosa Donor 29	rectum
39	chr4:99181000-99183600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr4:99181000-99183600	Active TSS	Breast Myoepithelial Primary Cells	Breast
41	chr4:99181000-99183800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
42	chr4:99181000-99183800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr4:99181000-99183800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr4:99181000-99183800	Active TSS	Fetal Brain Male	brain
45	chr4:99181000-99183800	Active TSS	Fetal Intestine Large	intestine
46	chr4:99181000-99183800	Active TSS	Fetal Stomach	stomach
47	chr4:99181000-99183800	Active TSS	Right Atrium	heart
48	chr4:99181000-99183800	Active TSS	GM12878-XiMat	blood
49	chr4:99181000-99183800	Active TSS	NHDF-Ad	bronchial
50	chr4:99181000-99184000	Active TSS	H1 Cell Line	embryonic stem cell

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