Variant report

Variant	rs60271600
Chromosome Location	chr12:120632899-120632900
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	TEAD4	chr12:120632259-120633217	ECC-1	luminal epithelium:	n/a	n/a
2	POLR2A	chr12:120632336-120634178	HCT-116	colon:	n/a	n/a
3	EP300	chr12:120632528-120633298	GM12878	blood:	n/a	chr12:120632624-120632633 chr12:120632808-120632824
4	TAF1	chr12:120632086-120633274	ECC-1	luminal epithelium:	n/a	n/a
5	NFIC	chr12:120632798-120633286	HepG2	liver:	n/a	n/a
6	ZNF384	chr12:120632348-120633999	K562	blood:	n/a	n/a
7	POLR2A	chr12:120632203-120632924	H1-neurons	neurons:	n/a	n/a
8	HCFC1	chr12:120631413-120634490	Hela-S3	cervix:	n/a	n/a
9	SP4	chr12:120632371-120632986	H1-hESC	embryonic stem cell:	n/a	n/a
10	MAZ	chr12:120632306-120632929	HepG2	liver:	n/a	chr12:120632554-120632563
11	CREB1	chr12:120632154-120633402	HepG2	liver:	n/a	n/a
12	MAX	chr12:120632265-120633230	SK-N-SH	brain:	n/a	chr12:120632554-120632563
13	ELK1	chr12:120632345-120633030	Hela-S3	cervix:	n/a	n/a
14	MAFK	chr12:120632736-120633092	HepG2	liver:	n/a	n/a
15	POLR2A	chr12:120632187-120633129	MCF-7	breast:	n/a	n/a
16	BCLAF1	chr12:120632248-120634467	K562	blood:	n/a	chr12:120632625-120632638 chr12:120632581-120632594 chr12:120632462-120632475 chr12:120632464-120632477 chr12:120632577-120632590
17	MAZ	chr12:120631909-120633289	IMR90	lung:	n/a	chr12:120632554-120632563
18	ELK1	chr12:120632218-120633203	K562	blood:	n/a	n/a
19	SIN3A	chr12:120631778-120633291	H1-hESC	embryonic stem cell:	n/a	chr12:120632233-120632246 chr12:120632462-120632473
20	RFX5	chr12:120632836-120633181	K562	blood:	n/a	n/a
21	POLR2A	chr12:120631371-120639781	PANC-1	pancreas:	n/a	n/a
22	BCL3	chr12:120632240-120634153	GM12878	blood:	n/a	chr12:120632625-120632638 chr12:120632581-120632594 chr12:120632462-120632475 chr12:120632464-120632477 chr12:120632577-120632590
23	TCF12	chr12:120632016-120633142	ECC-1	luminal epithelium:	n/a	n/a
24	TAF1	chr12:120632237-120632971	GM12878	blood:	n/a	n/a
25	CTCF	chr12:120632781-120633000	K562	blood:	n/a	n/a
26	MYC	chr12:120631638-120634210	K562	blood:	n/a	chr12:120632554-120632563 chr12:120634196-120634206
27	GABPA	chr12:120631739-120633613	A549	lung:	n/a	n/a
28	POLR2A	chr12:120632180-120634392	GM12878	blood:	n/a	n/a
29	NFATC1	chr12:120632249-120634334	GM12878	blood:	n/a	n/a
30	CHD1	chr12:120632263-120633382	H1-hESC	embryonic stem cell:	n/a	n/a
31	POLR2A	chr12:120632187-120634174	Raji	blood:	n/a	n/a
32	CHD1	chr12:120632872-120633331	GM12878	blood:	n/a	n/a
33	MAFF	chr12:120632667-120633211	HepG2	liver:	n/a	n/a
34	GABPA	chr12:120631983-120633236	HL-60	blood:	n/a	n/a
35	MAX	chr12:120632136-120633567	HepG2	liver:	n/a	chr12:120632554-120632563
36	POLR2A	chr12:120632048-120635920	MCF10A-Er-Src	breast:	n/a	n/a
37	POLR2A	chr12:120632029-120639863	Hela-S3	cervix:	n/a	n/a
38	PML	chr12:120632239-120633354	K562	blood:	n/a	chr12:120633279-120633287
39	BCL3	chr12:120632826-120633284	K562	blood:	n/a	n/a
40	TEAD4	chr12:120632311-120634578	K562	blood:	n/a	n/a
41	POLR2A	chr12:120632161-120634190	GM15510	blood:	n/a	n/a
42	TEAD4	chr12:120632684-120633478	HepG2	liver:	n/a	n/a
43	TBP	chr12:120632181-120633282	K562	blood:	n/a	n/a
44	ELF1	chr12:120632250-120633332	A549	lung:	n/a	chr12:120632535-120632546 chr12:120632535-120632544 chr12:120632536-120632545 chr12:120632624-120632636
45	FOS	chr12:120632375-120633154	HUVEC	blood vessel:	n/a	chr12:120632846-120632857 chr12:120632847-120632857 chr12:120632847-120632857 chr12:120632847-120632857 chr12:120632469-120632478
46	TAF1	chr12:120632083-120632939	ECC-1	luminal epithelium:	n/a	n/a
47	MAX	chr12:120632100-120633209	A549	lung:	n/a	chr12:120632554-120632563
48	BHLHE40	chr12:120632357-120633289	GM12878	blood:	n/a	chr12:120632464-120632480 chr12:120632622-120632638
49	POLR2A	chr12:120632039-120634607	HL-60	blood:	n/a	n/a
50	POLR2A	chr12:120632869-120633212	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:120628864..120642103-chr12:120725347..120732286,54	K562	blood:
2	chr12:120628211..120641965-chr12:120660551..120674110,39	K562	blood:
3	chr12:120553299..120556376-chr12:120632430..120634315,3	MCF-7	breast:
4	chr12:120632157..120632928-chr20:34329557..34330164,2	Hela-S3	cervix:
5	chr12:120551826..120556882-chr12:120630846..120640383,26	K562	blood:
6	chr12:120626707..120642605-chr12:120719450..120732919,96	MCF-7	breast:
7	chr12:120632625..120633570-chr15:23033849..23034537,2	NB4	blood:
8	chr1:149856699..149859213-chr12:120631502..120633814,2	K562	blood:
9	chr12:120573945..120575639-chr12:120632409..120634633,3	MCF-7	breast:
10	chr12:120609315..120613090-chr12:120629973..120633453,5	K562	blood:
11	chr12:120632678..120633360-chrX:133930768..133931430,2	HCT-116	colon:
12	chr12:120632665..120634375-chr12:120655462..120658221,2	K562	blood:
13	chr12:120600039..120601830-chr12:120632774..120634294,2	MCF-7	breast:
14	chr12:120574047..120576744-chr12:120631730..120634976,3	MCF-7	breast:
15	chr12:120629843..120633670-chr12:120702168..120705891,5	K562	blood:
16	chr12:120632627..120633205-chr6:27114567..27115227,2	Hela-S3	cervix:
17	chr12:120594749..120596361-chr12:120632172..120634549,2	K562	blood:
18	chr12:120631139..120640506-chr12:120724902..120734482,54	K562	blood:
19	chr12:120552488..120558210-chr12:120630092..120634088,8	MCF-7	breast:
20	chr12:120632252..120633121-chr19:39897386..39898105,2	Hela-S3	cervix:
21	chr12:120552161..120556177-chr12:120630368..120635589,11	K562	blood:

Variant related genes	Relation type
GCN1L1	TF binding region
ENSG00000200795	Chromatin interaction
ENSG00000089159	Chromatin interaction
ENSG00000156500	Chromatin interaction
ENSG00000131051	Chromatin interaction
ENSG00000263913	Chromatin interaction
ENSG00000184678	Chromatin interaction
ENSG00000202538	Chromatin interaction
ENSG00000184825	Chromatin interaction
ENSG00000140157	Chromatin interaction
ENSG00000089154	Chromatin interaction
ENSG00000123009	Chromatin interaction
ENSG00000197903	Chromatin interaction
ENSG00000128016	Chromatin interaction
ENSG00000184260	Chromatin interaction
ENSG00000111737	Chromatin interaction
ENSG00000156504	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10437836	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11065035	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11065036	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11065040	0.88[ASN][1000 genomes]
rs11833158	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11836049	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12305184	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12306075	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12310433	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12312562	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12320253	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12578300	0.98[EUR][1000 genomes]
rs2074540	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2238155	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2240314	0.80[EUR][1000 genomes]
rs2240315	0.88[EUR][1000 genomes]
rs2240317	0.91[EUR][1000 genomes]
rs2240318	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2240319	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2240320	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2240321	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2240322	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2240323	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2240325	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2269940	0.86[EUR][1000 genomes]
rs2269941	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2269943	0.87[EUR][1000 genomes]
rs2269944	0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2269945	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2283362	0.91[EUR][1000 genomes]
rs2286043	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2286044	0.83[EUR][1000 genomes]
rs2286045	0.90[EUR][1000 genomes]
rs2286049	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2286050	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2286051	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3742040	0.84[EUR][1000 genomes]
rs3815210	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4522230	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57546423	0.88[EUR][1000 genomes]
rs57780521	0.87[EUR][1000 genomes]
rs59601514	0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7133235	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7134706	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7135914	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7294892	0.87[EUR][1000 genomes]
rs7296380	0.96[ASN][1000 genomes]
rs7299429	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7301660	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7310175	0.90[ASN][1000 genomes]
rs7953741	0.80[EUR][1000 genomes]
rs7974732	0.88[ASN][1000 genomes]
rs7978061	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7978175	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9630281	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9651914	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3525916	chr12:120345352-120665045	Bivalent Enhancer Genic enhancers Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
2	esv3525917	chr12:120345352-120665045	Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
3	nsv899555	chr12:120519124-120840522	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	499 gene(s)	inside rSNPs	diseases
4	nsv519657	chr12:120533696-120676090	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
5	nsv560433	chr12:120533696-120676090	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
6	nsv832530	chr12:120586069-120758175	Flanking Active TSS Strong transcription Enhancers Genic enhancers Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	484 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	chr12:120631000-120633000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:120631000-120633000	Active TSS	HUES6 Cell Line	embryonic stem cell
3	chr12:120631000-120633400	Active TSS	H1 Cell Line	embryonic stem cell
4	chr12:120631000-120633400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr12:120631000-120633400	Active TSS	HUES64 Cell Line	embryonic stem cell
6	chr12:120631200-120633000	Active TSS	Sigmoid Colon	Sigmoid Colon
7	chr12:120631200-120633800	Active TSS	iPS-15b Cell Line	embryonic stem cell
8	chr12:120631400-120633000	Active TSS	NHDF-Ad	bronchial
9	chr12:120631400-120633200	Flanking Active TSS	Primary B cells from cord blood	blood
10	chr12:120631400-120633400	Active TSS	H9 Cell Line	embryonic stem cell
11	chr12:120631400-120633400	Active TSS	iPS-18 Cell Line	embryonic stem cell
12	chr12:120631400-120633400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
13	chr12:120631400-120633400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr12:120631600-120633000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr12:120631600-120633000	Active TSS	Esophagus	oesophagus
16	chr12:120631600-120633200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr12:120631600-120633200	Flanking Active TSS	Primary hematopoietic stem cells	blood
18	chr12:120631600-120633200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
19	chr12:120631600-120633400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
20	chr12:120631600-120634000	Active TSS	iPS-20b Cell Line	embryonic stem cell
21	chr12:120631800-120633000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr12:120631800-120633000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr12:120631800-120633000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr12:120631800-120633000	Active TSS	Breast Myoepithelial Primary Cells	Breast
25	chr12:120631800-120633000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr12:120631800-120633000	Active TSS	Aorta	Aorta
27	chr12:120631800-120633000	Active TSS	Gastric	stomach
28	chr12:120631800-120633000	Active TSS	Ovary	ovary
29	chr12:120631800-120633000	Active TSS	Pancreas	Pancrea
30	chr12:120631800-120633000	Active TSS	Small Intestine	intestine
31	chr12:120631800-120633200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
32	chr12:120631800-120633200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
33	chr12:120631800-120633400	Active TSS	ES-I3 Cell Line	embryonic stem cell
34	chr12:120631800-120633400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
35	chr12:120631800-120633400	Active TSS	Psoas Muscle	Psoas
36	chr12:120632000-120633000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr12:120632000-120633000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr12:120632000-120633000	Active TSS	Fetal Kidney	kidney
39	chr12:120632000-120633000	Active TSS	Pancreatic Islets	Pancreatic Islet
40	chr12:120632000-120633000	Active TSS	GM12878-XiMat	blood
41	chr12:120632000-120633200	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr12:120632000-120633400	Active TSS	Fetal Brain Female	brain
43	chr12:120632200-120633000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr12:120632200-120633000	Active TSS	Primary T killer memory cells from peripheral blood	blood
45	chr12:120632400-120633200	Transcr. at gene 5' and 3'	Right Atrium	heart
46	chr12:120632400-120633600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr12:120632600-120633000	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr12:120632600-120633000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr12:120632600-120633200	Flanking Active TSS	Primary B cells from peripheral blood	blood
50	chr12:120632600-120633200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood

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