Variant report

Variant	rs2274228
Chromosome Location	chr1:179052002-179052003
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	POLR2A	chr1:179050648-179052242	MCF-7	breast:	n/a	n/a
2	POLR2A	chr1:179050421-179053208	GM12892	blood:	n/a	n/a
3	SIN3AK20	chr1:179050684-179052245	PANC-1	pancreas:	n/a	n/a
4	USF1	chr1:179051896-179052310	A549	lung:	n/a	chr1:179052117-179052128
5	POLR2A	chr1:179050620-179052113	K562	blood:	n/a	n/a
6	TCF12	chr1:179050456-179052398	A549	lung:	n/a	n/a
7	USF2	chr1:179051936-179052292	HepG2	liver:	n/a	chr1:179052117-179052128
8	RCOR1	chr1:179051870-179052181	HepG2	liver:	n/a	n/a
9	POLR2A	chr1:179050485-179052344	K562	blood:	n/a	n/a
10	MXI1	chr1:179050568-179052638	SK-N-SH	brain:	n/a	chr1:179051135-179051150
11	SIN3AK20	chr1:179051702-179052240	SK-N-SH	brain:	n/a	n/a
12	POLR2A	chr1:179049925-179052426	GM12878	blood:	n/a	n/a
13	MAZ	chr1:179050435-179052538	IMR90	lung:	n/a	chr1:179051658-179051668 chr1:179052196-179052205 chr1:179050699-179050708
14	POLR2A	chr1:179050547-179052186	Hela-S3	cervix:	n/a	n/a
15	POLR2A	chr1:179051741-179052465	GM12892	blood:	n/a	n/a
16	MTA3	chr1:179050015-179052498	GM12878	blood:	n/a	n/a
17	SIN3AK20	chr1:179050408-179052408	MCF-7	breast:	n/a	n/a
18	MAX	chr1:179051826-179052309	A549	lung:	n/a	chr1:179052196-179052205
19	UBTF	chr1:179050649-179052011	K562	blood:	n/a	n/a
20	POLR2A	chr1:179051762-179052428	GM12891	blood:	n/a	n/a
21	MYC	chr1:179051937-179052305	MCF10A-Er-Src	breast:	n/a	chr1:179052196-179052205
22	PML	chr1:179051709-179052569	GM12878	blood:	n/a	n/a
23	MYC	chr1:179050372-179052402	K562	blood:	n/a	chr1:179051658-179051668 chr1:179052196-179052205 chr1:179050699-179050708
24	MAX	chr1:179050568-179052474	HepG2	liver:	n/a	chr1:179051658-179051668 chr1:179052196-179052205 chr1:179050699-179050708
25	USF1	chr1:179051862-179052347	H1-hESC	embryonic stem cell:	n/a	chr1:179052117-179052128
26	MAX	chr1:179050645-179052385	SK-N-SH	brain:	n/a	chr1:179051658-179051668 chr1:179052196-179052205 chr1:179050699-179050708
27	E2F6	chr1:179050503-179052340	H1-hESC	embryonic stem cell:	n/a	chr1:179051662-179051672 chr1:179050827-179050839 chr1:179051754-179051763 chr1:179050828-179050839
28	CTCF	chr1:179051920-179052070	GM12864	blood:	n/a	n/a
29	PAX5	chr1:179051734-179052015	GM12878	blood:	n/a	n/a
30	POLR2A	chr1:179049821-179052584	GM12878	blood:	n/a	n/a
31	POLR2A	chr1:179049868-179052441	Hela-S3	cervix:	n/a	n/a
32	MYC	chr1:179051960-179052226	GM12878	blood:	n/a	chr1:179052196-179052205
33	MAX	chr1:179050625-179052388	H1-hESC	embryonic stem cell:	n/a	chr1:179051658-179051668 chr1:179052196-179052205 chr1:179050699-179050708
34	USF1	chr1:179051982-179052256	GM12878	blood:	n/a	chr1:179052117-179052128
35	MAX	chr1:179051865-179052330	NB4	blood:	n/a	chr1:179052196-179052205
36	RCOR1	chr1:179050593-179052383	K562	blood:	n/a	n/a
37	SMARCB1	chr1:179050430-179052306	Hela-S3	cervix:	n/a	n/a
38	POLR2A	chr1:179050072-179053327	GM19193	blood:	n/a	n/a
39	REST	chr1:179050661-179052264	H1-neurons	neurons:	n/a	chr1:179051054-179051068 chr1:179051655-179051668 chr1:179051596-179051609 chr1:179051054-179051074
40	POLR2A	chr1:179049835-179053382	GM12891	blood:	n/a	n/a
41	POLR2A	chr1:179050836-179052207	H1-neurons	neurons:	n/a	n/a
42	MAX	chr1:179050667-179052364	Hela-S3	cervix:	n/a	chr1:179051658-179051668 chr1:179052196-179052205 chr1:179050699-179050708
43	USF2	chr1:179051884-179052329	Hela-S3	cervix:	n/a	chr1:179052117-179052128
44	ELF1	chr1:179050545-179052446	GM12878	blood:	n/a	chr1:179051655-179051667 chr1:179050813-179050824
45	MAX	chr1:179050464-179052634	A549	lung:	n/a	chr1:179051658-179051668 chr1:179052196-179052205 chr1:179050699-179050708
46	E2F6	chr1:179051726-179052275	K562	blood:	n/a	chr1:179051754-179051763
47	POLR2A	chr1:179050656-179052179	HUVEC	blood vessel:	n/a	n/a
48	USF1	chr1:179051920-179052316	K562	blood:	n/a	chr1:179052117-179052128
49	POLR2A	chr1:179051922-179052069	MCF10A-Er-Src	breast:	n/a	n/a
50	HA-E2F1	chr1:179050700-179052275	Hela-S3	cervix:	n/a	chr1:179051662-179051672 chr1:179050827-179050839 chr1:179051754-179051763

No.	Distal block	Cell Line	Cell type
1	chr1:178903732..178906494-chr1:179051387..179053146,2	K562	blood:
2	chr1:179049954..179052769-chr1:179333565..179337813,7	MCF-7	breast:
3	chr1:179050855..179052664-chr1:179261724..179264711,2	K562	blood:
4	chr1:179051673..179054487-chr1:179062645..179065575,2	K562	blood:
5	chr1:179051978..179053865-chr1:179066668..179068883,2	K562	blood:
6	chr1:179050855..179053575-chr1:179263211..179266215,3	K562	blood:
7	chr1:179051431..179053361-chr1:179162011..179164683,2	MCF-7	breast:
8	chr1:178837797..178839494-chr1:179049948..179052882,2	K562	blood:
9	chr1:178993182..178999783-chr1:179045102..179052535,14	MCF-7	breast:
10	chr1:179048972..179052099-chr1:179331450..179336701,5	MCF-7	breast:
11	chr1:179049424..179053663-chr1:179259743..179264339,5	MCF-7	breast:
12	chr1:179049160..179052033-chr1:179333339..179335895,3	K562	blood:
13	chr1:178994647..178996585-chr1:179051040..179053373,3	MCF-7	breast:

Variant related genes	Relation type
TOR3A	TF binding region
ENSG00000116194	Chromatin interaction
ENSG00000057252	Chromatin interaction
ENSG00000116199	Chromatin interaction
ENSG00000263633	Chromatin interaction
ENSG00000162779	Chromatin interaction

rs_ID	r²[population]
rs10157463	0.83[ASN][1000 genomes]
rs10157885	0.83[ASN][1000 genomes]
rs10158768	0.97[ASN][1000 genomes]
rs10913675	0.86[ASN][1000 genomes]
rs10913687	0.86[ASN][1000 genomes]
rs11808217	0.83[ASN][1000 genomes]
rs12066589	0.86[ASN][1000 genomes]
rs12067262	0.86[ASN][1000 genomes]
rs12071751	0.83[ASN][1000 genomes]
rs12076957	0.86[ASN][1000 genomes]
rs12079974	0.83[ASN][1000 genomes]
rs12083856	0.83[ASN][1000 genomes]
rs12086225	0.81[ASN][1000 genomes]
rs12089188	0.86[ASN][1000 genomes]
rs12091355	0.83[ASN][1000 genomes]
rs12143004	0.88[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs16853551	0.83[ASN][1000 genomes]
rs16853619	0.86[ASN][1000 genomes]
rs17277358	0.85[ASN][1000 genomes]
rs17361990	0.91[ASN][1000 genomes]
rs17362128	0.85[ASN][1000 genomes]
rs2017688	0.85[ASN][1000 genomes]
rs2025580	0.81[AFR][1000 genomes]
rs2147766	0.89[AFR][1000 genomes]
rs2274230	0.85[ASN][1000 genomes]
rs28914474	0.83[ASN][1000 genomes]
rs28914485	0.83[ASN][1000 genomes]
rs3753532	0.85[ASN][1000 genomes]
rs3766631	0.86[ASN][1000 genomes]
rs3766633	0.83[ASN][1000 genomes]
rs3766634	0.83[ASN][1000 genomes]
rs4456058	0.94[AFR][1000 genomes]
rs45499094	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55642919	0.83[ASN][1000 genomes]
rs55697941	0.82[AMR][1000 genomes]
rs55781720	0.94[AFR][1000 genomes]
rs55825882	0.85[ASN][1000 genomes]
rs55920203	0.85[ASN][1000 genomes]
rs56107346	0.89[AFR][1000 genomes]
rs56382583	0.83[ASN][1000 genomes]
rs57215421	0.83[ASN][1000 genomes]
rs58726191	0.86[ASN][1000 genomes]
rs7516491	0.81[ASN][1000 genomes]
rs7519023	0.81[ASN][1000 genomes]
rs7544822	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs7552470	0.83[ASN][1000 genomes]
rs9650997	0.85[ASN][1000 genomes]
rs9724754	0.85[ASN][1000 genomes]
rs9725888	0.88[ASN][1000 genomes]
rs9726948	0.86[ASN][1000 genomes]
rs9730271	0.97[ASN][1000 genomes]

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179050200-179052400	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr1:179050200-179052400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
3	chr1:179050200-179052600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr1:179050400-179052400	Active TSS	Pancreatic Islets	Pancreatic Islet
5	chr1:179050400-179053000	Active TSS	H9 Cell Line	embryonic stem cell
6	chr1:179050600-179052200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr1:179050600-179052200	Active TSS	Aorta	Aorta
8	chr1:179050600-179052200	Active TSS	Fetal Intestine Large	intestine
9	chr1:179050600-179052200	Active TSS	Ovary	ovary
10	chr1:179050600-179052200	Active TSS	Sigmoid Colon	Sigmoid Colon
11	chr1:179050600-179052200	Active TSS	Small Intestine	intestine
12	chr1:179050600-179052400	Flanking Active TSS	Primary hematopoietic stem cells	blood
13	chr1:179050600-179052400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr1:179050600-179052400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
15	chr1:179050600-179052600	Active TSS	NHLF	lung
16	chr1:179050800-179052200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr1:179050800-179052200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr1:179050800-179052200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
19	chr1:179050800-179052200	Active TSS	Brain Substantia Nigra	brain
20	chr1:179050800-179052200	Active TSS	Rectal Smooth Muscle	rectum
21	chr1:179050800-179052400	Active TSS	Placenta Amnion	Placenta Amnion
22	chr1:179050800-179052600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr1:179050800-179052600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
24	chr1:179050800-179052600	Active TSS	Duodenum Smooth Muscle	Duodenum
25	chr1:179050800-179052600	Active TSS	NHDF-Ad	bronchial
26	chr1:179051000-179052200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr1:179051000-179052200	Active TSS	iPS-15b Cell Line	embryonic stem cell
28	chr1:179051000-179052200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr1:179051000-179052200	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
30	chr1:179051000-179052200	Active TSS	Fetal Brain Male	brain
31	chr1:179051000-179052200	Active TSS	Hela-S3	cervix
32	chr1:179051000-179052400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr1:179051000-179052400	Active TSS	Fetal Kidney	kidney
34	chr1:179051000-179052600	Active TSS	A549	lung
35	chr1:179051000-179052800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr1:179051000-179052800	Active TSS	Osteobl	bone
37	chr1:179051000-179053000	Active TSS	GM12878-XiMat	blood
38	chr1:179051000-179053000	Active TSS	HSMMtube	muscle
39	chr1:179051200-179052800	Active TSS	HSMM	muscle
40	chr1:179051400-179052600	Flanking Active TSS	Primary B cells from cord blood	blood
41	chr1:179051400-179052600	Flanking Active TSS	Adipose Nuclei	Adipose
42	chr1:179051800-179052200	Flanking Active TSS	H1 Cell Line	embryonic stem cell
43	chr1:179051800-179052200	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr1:179051800-179052200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
45	chr1:179051800-179052200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
46	chr1:179051800-179052200	Flanking Active TSS	Placenta	Placenta
47	chr1:179051800-179052200	Flanking Active TSS	Spleen	Spleen
48	chr1:179051800-179052400	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr1:179051800-179052400	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr1:179051800-179052400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived

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