Variant report

Variant	rs7310175
Chromosome Location	chr12:120632729-120632730
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	EGR1	chr12:120632229-120632807	ECC-1	luminal epithelium:	n/a	n/a
2	TEAD4	chr12:120632259-120633217	ECC-1	luminal epithelium:	n/a	n/a
3	ZBTB7A	chr12:120632300-120632898	K562	blood:	n/a	n/a
4	POLR2A	chr12:120632336-120634178	HCT-116	colon:	n/a	n/a
5	EP300	chr12:120632528-120633298	GM12878	blood:	n/a	chr12:120632624-120632633 chr12:120632808-120632824
6	TAF1	chr12:120632086-120633274	ECC-1	luminal epithelium:	n/a	n/a
7	ZNF384	chr12:120632348-120633999	K562	blood:	n/a	n/a
8	POLR2A	chr12:120632203-120632924	H1-neurons	neurons:	n/a	n/a
9	TCF3	chr12:120632370-120632788	GM12878	blood:	n/a	n/a
10	HCFC1	chr12:120631413-120634490	Hela-S3	cervix:	n/a	n/a
11	SP4	chr12:120632371-120632986	H1-hESC	embryonic stem cell:	n/a	n/a
12	MAZ	chr12:120632306-120632929	HepG2	liver:	n/a	chr12:120632554-120632563
13	CREB1	chr12:120632154-120633402	HepG2	liver:	n/a	n/a
14	MAX	chr12:120632265-120633230	SK-N-SH	brain:	n/a	chr12:120632554-120632563
15	ELK1	chr12:120632345-120633030	Hela-S3	cervix:	n/a	n/a
16	POLR2A	chr12:120632187-120633129	MCF-7	breast:	n/a	n/a
17	YY1	chr12:120632147-120632793	H1-hESC	embryonic stem cell:	n/a	chr12:120632462-120632473 chr12:120632635-120632649 chr12:120632296-120632310
18	BCLAF1	chr12:120632248-120634467	K562	blood:	n/a	chr12:120632625-120632638 chr12:120632581-120632594 chr12:120632462-120632475 chr12:120632464-120632477 chr12:120632577-120632590
19	MAZ	chr12:120631909-120633289	IMR90	lung:	n/a	chr12:120632554-120632563
20	ELK1	chr12:120632218-120633203	K562	blood:	n/a	n/a
21	EGR1	chr12:120632331-120632821	ECC-1	luminal epithelium:	n/a	n/a
22	PAX5	chr12:120632283-120632736	GM12878	blood:	n/a	n/a
23	SIN3A	chr12:120631778-120633291	H1-hESC	embryonic stem cell:	n/a	chr12:120632233-120632246 chr12:120632462-120632473
24	POLR2A	chr12:120631371-120639781	PANC-1	pancreas:	n/a	n/a
25	BCL3	chr12:120632240-120634153	GM12878	blood:	n/a	chr12:120632625-120632638 chr12:120632581-120632594 chr12:120632462-120632475 chr12:120632464-120632477 chr12:120632577-120632590
26	TCF12	chr12:120632016-120633142	ECC-1	luminal epithelium:	n/a	n/a
27	TAF1	chr12:120632237-120632971	GM12878	blood:	n/a	n/a
28	EGR1	chr12:120632264-120632745	GM12878	blood:	n/a	n/a
29	MYC	chr12:120631638-120634210	K562	blood:	n/a	chr12:120632554-120632563 chr12:120634196-120634206
30	ZEB1	chr12:120632198-120632746	GM12878	blood:	n/a	chr12:120632475-120632488 chr12:120632476-120632485
31	GABPA	chr12:120631739-120633613	A549	lung:	n/a	n/a
32	POLR2A	chr12:120632180-120634392	GM12878	blood:	n/a	n/a
33	NFATC1	chr12:120632249-120634334	GM12878	blood:	n/a	n/a
34	POLR2A	chr12:120632210-120632859	A549	lung:	n/a	n/a
35	CHD1	chr12:120632263-120633382	H1-hESC	embryonic stem cell:	n/a	n/a
36	POLR2A	chr12:120632187-120634174	Raji	blood:	n/a	n/a
37	EP300	chr12:120632294-120632785	T-47D	breast:	n/a	chr12:120632624-120632633
38	MAFF	chr12:120632667-120633211	HepG2	liver:	n/a	n/a
39	GABPA	chr12:120631983-120633236	HL-60	blood:	n/a	n/a
40	EP300	chr12:120632295-120632784	T-47D	breast:	n/a	chr12:120632624-120632633
41	MAX	chr12:120632136-120633567	HepG2	liver:	n/a	chr12:120632554-120632563
42	SIN3A	chr12:120632118-120632824	GM12878	blood:	n/a	chr12:120632233-120632246 chr12:120632462-120632473
43	POLR2A	chr12:120632048-120635920	MCF10A-Er-Src	breast:	n/a	n/a
44	POLR2A	chr12:120632029-120639863	Hela-S3	cervix:	n/a	n/a
45	PML	chr12:120632239-120633354	K562	blood:	n/a	chr12:120633279-120633287
46	TEAD4	chr12:120632311-120634578	K562	blood:	n/a	n/a
47	POLR2A	chr12:120632161-120634190	GM15510	blood:	n/a	n/a
48	ETS1	chr12:120632121-120632859	K562	blood:	n/a	chr12:120632585-120632596 chr12:120632516-120632533 chr12:120632522-120632532 chr12:120632516-120632533
49	TEAD4	chr12:120632684-120633478	HepG2	liver:	n/a	n/a
50	TBP	chr12:120632181-120633282	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:120628864..120642103-chr12:120725347..120732286,54	K562	blood:
2	chr12:120632218..120632835-chr5:43121680..43122197,2	Hela-S3	cervix:
3	chr12:120628211..120641965-chr12:120660551..120674110,39	K562	blood:
4	chr12:120553299..120556376-chr12:120632430..120634315,3	MCF-7	breast:
5	chr12:120632157..120632928-chr20:34329557..34330164,2	Hela-S3	cervix:
6	chr12:120551826..120556882-chr12:120630846..120640383,26	K562	blood:
7	chr12:120626707..120642605-chr12:120719450..120732919,96	MCF-7	breast:
8	chr12:120632625..120633570-chr15:23033849..23034537,2	NB4	blood:
9	chr1:149856699..149859213-chr12:120631502..120633814,2	K562	blood:
10	chr12:120573945..120575639-chr12:120632409..120634633,3	MCF-7	breast:
11	chr12:120609315..120613090-chr12:120629973..120633453,5	K562	blood:
12	chr12:120632678..120633360-chrX:133930768..133931430,2	HCT-116	colon:
13	chr12:120632665..120634375-chr12:120655462..120658221,2	K562	blood:
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:
22	chr1:25558678..25559549-chr12:120632155..120632833,2	HCT-116	colon:

Variant related genes	Relation type
GCN1L1	TF binding region
ENSG00000172262	Chromatin interaction
ENSG00000140157	Chromatin interaction
ENSG00000156500	Chromatin interaction
ENSG00000111737	Chromatin interaction
ENSG00000089159	Chromatin interaction
ENSG00000200795	Chromatin interaction
ENSG00000184825	Chromatin interaction
ENSG00000131051	Chromatin interaction
ENSG00000117614	Chromatin interaction
ENSG00000263913	Chromatin interaction
ENSG00000156504	Chromatin interaction
ENSG00000123009	Chromatin interaction
ENSG00000184678	Chromatin interaction
ENSG00000197903	Chromatin interaction
ENSG00000128016	Chromatin interaction
ENSG00000184260	Chromatin interaction
ENSG00000202538	Chromatin interaction
ENSG00000089154	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11065036	0.87[ASN][1000 genomes]
rs11065040	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11833158	0.86[ASN][1000 genomes]
rs12305184	0.86[ASN][1000 genomes]
rs12306075	0.86[ASN][1000 genomes]
rs12320253	0.86[ASN][1000 genomes]
rs2074540	0.89[ASN][1000 genomes]
rs2240324	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2240325	0.87[ASN][1000 genomes]
rs2269945	0.86[ASN][1000 genomes]
rs2286050	0.87[ASN][1000 genomes]
rs2286051	0.86[ASN][1000 genomes]
rs3742039	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4522230	0.87[ASN][1000 genomes]
rs60271600	0.90[ASN][1000 genomes]
rs7133235	0.84[ASN][1000 genomes]
rs7134706	0.87[ASN][1000 genomes]
rs7135914	0.86[ASN][1000 genomes]
rs7296380	0.86[ASN][1000 genomes]
rs7299429	0.88[ASN][1000 genomes]
rs7960120	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7974732	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7978061	0.87[ASN][1000 genomes]
rs7978175	0.82[ASN][1000 genomes]
rs9630281	0.85[ASN][1000 genomes]
rs9651914	0.87[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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7310175	GCN1L1	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:120631000-120632800	Active TSS	HUES48 Cell Line	embryonic stem cell
2	chr12:120631000-120633000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr12:120631000-120633000	Active TSS	HUES6 Cell Line	embryonic stem cell
4	chr12:120631000-120633400	Active TSS	H1 Cell Line	embryonic stem cell
5	chr12:120631000-120633400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr12:120631000-120633400	Active TSS	HUES64 Cell Line	embryonic stem cell
7	chr12:120631200-120632800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr12:120631200-120633000	Active TSS	Sigmoid Colon	Sigmoid Colon
9	chr12:120631200-120633800	Active TSS	iPS-15b Cell Line	embryonic stem cell
10	chr12:120631400-120632800	Active TSS	Fetal Intestine Large	intestine
11	chr12:120631400-120632800	Active TSS	HSMMtube	muscle
12	chr12:120631400-120632800	Active TSS	NHLF	lung
13	chr12:120631400-120633000	Active TSS	NHDF-Ad	bronchial
14	chr12:120631400-120633200	Flanking Active TSS	Primary B cells from cord blood	blood
15	chr12:120631400-120633400	Active TSS	H9 Cell Line	embryonic stem cell
16	chr12:120631400-120633400	Active TSS	iPS-18 Cell Line	embryonic stem cell
17	chr12:120631400-120633400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
18	chr12:120631400-120633400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr12:120631600-120632800	Active TSS	Fetal Muscle Trunk	muscle
20	chr12:120631600-120632800	Active TSS	Left Ventricle	heart
21	chr12:120631600-120632800	Bivalent/Poised TSS	HepG2	liver
22	chr12:120631600-120633000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr12:120631600-120633000	Active TSS	Esophagus	oesophagus
24	chr12:120631600-120633200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr12:120631600-120633200	Flanking Active TSS	Primary hematopoietic stem cells	blood
26	chr12:120631600-120633200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
27	chr12:120631600-120633400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
28	chr12:120631600-120634000	Active TSS	iPS-20b Cell Line	embryonic stem cell
29	chr12:120631800-120632800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr12:120631800-120632800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr12:120631800-120632800	Active TSS	Fetal Intestine Small	intestine
32	chr12:120631800-120632800	Active TSS	Rectal Mucosa Donor 29	rectum
33	chr12:120631800-120632800	Active TSS	Right Ventricle	heart
34	chr12:120631800-120632800	Active TSS	A549	lung
35	chr12:120631800-120632800	Active TSS	K562	blood
36	chr12:120631800-120632800	Active TSS	NHEK	skin
37	chr12:120631800-120633000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr12:120631800-120633000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr12:120631800-120633000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr12:120631800-120633000	Active TSS	Breast Myoepithelial Primary Cells	Breast
41	chr12:120631800-120633000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr12:120631800-120633000	Active TSS	Aorta	Aorta
43	chr12:120631800-120633000	Active TSS	Gastric	stomach
44	chr12:120631800-120633000	Active TSS	Ovary	ovary
45	chr12:120631800-120633000	Active TSS	Pancreas	Pancrea
46	chr12:120631800-120633000	Active TSS	Small Intestine	intestine
47	chr12:120631800-120633200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
48	chr12:120631800-120633200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
49	chr12:120631800-120633400	Active TSS	ES-I3 Cell Line	embryonic stem cell
50	chr12:120631800-120633400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood

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