Variant report

Variant	rs2279559
Chromosome Location	chr12:46767175-46767176
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	RELA	chr12:46766330-46767803	GM15510	blood:	n/a	n/a
2	SIX5	chr12:46765523-46767198	A549	lung:	n/a	n/a
3	POLR2A	chr12:46767029-46767677	HCT-116	colon:	n/a	n/a
4	MYC	chr12:46764918-46767690	NB4	blood:	n/a	chr12:46767168-46767177 chr12:46765212-46765221 chr12:46766078-46766088 chr12:46765212-46765221 chr12:46765212-46765221 chr12:46765210-46765223
5	ZMIZ1	chr12:46766126-46767432	K562	blood:	n/a	n/a
6	POLR2A	chr12:46756521-46767732	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr12:46764987-46767683	HCT-116	colon:	n/a	n/a
8	REST	chr12:46764583-46767732	H1-neurons	neurons:	n/a	chr12:46766079-46766092 chr12:46766010-46766023 chr12:46765717-46765727 chr12:46765134-46765147 chr12:46767136-46767144
9	POLR2A	chr12:46760573-46767926	Hela-S3	cervix:	n/a	n/a
10	RAD21	chr12:46767152-46767638	SK-N-SH_RA	brain:	n/a	n/a
11	POLR2A	chr12:46750482-46767845	Hela-S3	cervix:	n/a	n/a
12	MAZ	chr12:46764964-46768004	K562	blood:	n/a	chr12:46767168-46767177 chr12:46765212-46765221 chr12:46766078-46766088 chr12:46765212-46765221 chr12:46765212-46765221 chr12:46765210-46765223
13	YY1	chr12:46766961-46767258	SK-N-SH_RA	brain:	n/a	n/a
14	SP1	chr12:46764683-46767225	A549	lung:	n/a	chr12:46766079-46766088 chr12:46766228-46766242 chr12:46766606-46766618 chr12:46766227-46766239 chr12:46766606-46766617 chr12:46766606-46766618 chr12:46766228-46766237 chr12:46766077-46766089 chr12:46765290-46765301 chr12:46766077-46766089 chr12:46766027-46766039 chr12:46766662-46766673 chr12:46766229-46766238 chr12:46765308-46765319 chr12:46766227-46766239 chr12:46766029-46766038 chr12:46766228-46766238 chr12:46766078-46766087
15	POLR2A	chr12:46754517-46767857	HepG2	liver:	n/a	n/a
16	REST	chr12:46764385-46767290	A549	lung:	n/a	chr12:46766079-46766092 chr12:46766010-46766023 chr12:46765717-46765727 chr12:46765134-46765147 chr12:46767136-46767144
17	POLR2A	chr12:46750751-46768006	HepG2	liver:	n/a	n/a
18	SIN3A	chr12:46767067-46767255	GM12878	blood:	n/a	n/a
19	MAX	chr12:46764817-46768138	K562	blood:	n/a	chr12:46767168-46767177 chr12:46765212-46765221 chr12:46766078-46766088 chr12:46765212-46765221 chr12:46765212-46765221 chr12:46765210-46765223
20	CHD1	chr12:46756240-46768821	IMR90	lung:	n/a	chr12:46765445-46765455 chr12:46766470-46766477 chr12:46768496-46768506 chr12:46768499-46768509
21	SP1	chr12:46764541-46768317	HCT-116	colon:	n/a	chr12:46766079-46766088 chr12:46766228-46766242 chr12:46766606-46766618 chr12:46766227-46766239 chr12:46766606-46766617 chr12:46766606-46766618 chr12:46766228-46766237 chr12:46766077-46766089 chr12:46765290-46765301 chr12:46766077-46766089 chr12:46766027-46766039 chr12:46766662-46766673 chr12:46766229-46766238 chr12:46765308-46765319 chr12:46766227-46766239 chr12:46766029-46766038 chr12:46766228-46766238 chr12:46766078-46766087
22	MAX	chr12:46764727-46768497	Hela-S3	cervix:	n/a	chr12:46767168-46767177 chr12:46765212-46765221 chr12:46766078-46766088 chr12:46765212-46765221 chr12:46765212-46765221 chr12:46765210-46765223
23	MYBL2	chr12:46764155-46767467	HepG2	liver:	n/a	n/a
24	MAX	chr12:46764491-46768176	HCT-116	colon:	n/a	chr12:46767168-46767177 chr12:46765212-46765221 chr12:46766078-46766088 chr12:46765212-46765221 chr12:46765212-46765221 chr12:46765210-46765223
25	CTBP2	chr12:46766812-46767914	H1-hESC	embryonic stem cell:	n/a	n/a
26	TAF1	chr12:46764814-46767518	Hela-S3	cervix:	n/a	n/a
27	SMC3	chr12:46764771-46768414	Hela-S3	cervix:	n/a	chr12:46765660-46765670
28	GTF2F1	chr12:46766297-46768001	Hela-S3	cervix:	n/a	n/a
29	POLR2A	chr12:46767002-46767495	K562	blood:	n/a	n/a
30	EP300	chr12:46766302-46767243	K562	blood:	n/a	n/a
31	TCF7L2	chr12:46764867-46768709	Hela-S3	cervix:	n/a	n/a
32	JUN	chr12:46764717-46768457	K562	blood:	n/a	n/a
33	TAF1	chr12:46764855-46767572	H1-hESC	embryonic stem cell:	n/a	n/a
34	POLR2A	chr12:46767029-46767516	K562	blood:	n/a	n/a
35	POLR2A	chr12:46754387-46768013	PANC-1	pancreas:	n/a	n/a
36	MXI1	chr12:46764789-46767849	Hela-S3	cervix:	n/a	chr12:46765211-46765220
37	YY1	chr12:46766860-46767563	H1-hESC	embryonic stem cell:	n/a	chr12:46767317-46767328
38	HEY1	chr12:46767018-46767455	K562	blood:	n/a	n/a
39	POLR2A	chr12:46767162-46767452	MCF-7	breast:	n/a	n/a
40	POLR2A	chr12:46754499-46767455	HUVEC	blood vessel:	n/a	n/a
41	ZBTB7A	chr12:46764828-46767207	ECC-1	luminal epithelium:	n/a	chr12:46765443-46765452 chr12:46766087-46766096
42	POLR2A	chr12:46767084-46767496	H1-hESC	embryonic stem cell:	n/a	n/a
43	POLR2A	chr12:46764772-46767677	K562	blood:	n/a	n/a
44	ELK1	chr12:46767051-46767292	Hela-S3	cervix:	n/a	n/a
45	SMARCC2	chr12:46766804-46767862	Hela-S3	cervix:	n/a	n/a
46	UBTF	chr12:46764783-46767582	K562	blood:	n/a	n/a
47	RCOR1	chr12:46766340-46767199	GM12878	blood:	n/a	n/a
48	POLR2A	chr12:46767082-46767559	HUVEC	blood vessel:	n/a	n/a
49	YY1	chr12:46767067-46767458	HepG2	liver:	n/a	chr12:46767317-46767328
50	CHD1	chr12:46767123-46767320	GM12878	blood:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:46767132-46767182	HPAEpiC	pulmonary alveolar:	n/a
2	chr12:46767132-46767182	ovcar-3	ovarian:	n/a
3	chr12:46767132-46767182	NHBE	bronchial:	n/a
4	chr12:46767132-46767182	SAEC	small airway:	n/a
5	chr12:46767132-46767182	HEK293	kidney:	embryo
6	chr12:46767132-46767182	ProgFib	skin:	n/a
7	chr12:46767132-46767182	NHDF-neo	bronchial:	n/a
8	chr12:46767132-46767182	HCM	heart:	n/a
9	chr12:46767132-46767182	HUVEC	blood vessel:	n/a
10	chr12:46767132-46767182	CMK	blood:	n/a
11	chr12:46767132-46767182	SK-N-SH_RA	brain:	n/a
12	chr12:46767132-46767182	AG09309	skin:	n/a
13	chr12:46767132-46767182	AG10803	skin:	n/a
14	chr12:46767132-46767182	HCF	heart:	n/a
15	chr12:46767132-46767182	HRPEpiC	eye:	n/a
16	chr12:46767132-46767182	HNPCEpiC	eye:	n/a
17	chr12:46767132-46767182	HL-60	blood:	n/a
18	chr12:46767132-46767182	AG09319	gingival:	n/a
19	chr12:46767132-46767182	PrEC	prostate:	n/a
20	chr12:46767132-46767182	K562	blood:	n/a
21	chr12:46767132-46767182	SKMC	muscle:	n/a
22	chr12:46767132-46767182	RPTEC	kidney:	n/a
23	chr12:46767132-46767182	SK-N-MC	brain:	n/a
24	chr12:46767132-46767182	PFSK-1	brain:	n/a
25	chr12:46767132-46767182	A549	lung:	n/a
26	chr12:46767132-46767182	BJ	skin:	n/a
27	chr12:46767132-46767182	T-47D	breast:	n/a
28	chr12:46767132-46767182	NT2-D1	testis:	n/a
29	chr12:46767132-46767182	HIPEpiC	eye:	n/a
30	chr12:46767132-46767182	GM12892	blood:	n/a
31	chr12:46767132-46767182	Hepatocyte	liver:	n/a
32	chr12:46767132-46767182	Hela-S3	cervix:	n/a
33	chr12:46767132-46767182	HRE	kidney:	n/a
34	chr12:46767132-46767182	PANC-1	pancreas:	n/a
35	chr12:46767132-46767182	BE2_C	brain:	n/a
36	chr12:46767132-46767182	ECC-1	luminal epithelium:	n/a
37	chr12:46767132-46767182	HCPEpiC	choroid plexus:	n/a
38	chr12:46767132-46767182	SK-N-SH	brain:	n/a
39	chr12:46767132-46767182	AG04449	skin:	fetal
40	chr12:46767132-46767182	HAEpiC	amniotic membrane:	n/a
41	chr12:46767132-46767182	U87	brain:	n/a
42	chr12:46767132-46767182	HRCEpiC	kidney:	n/a
43	chr12:46767132-46767182	LNCaP	prostate:	n/a
44	chr12:46767132-46767182	HMEC	breast:	n/a
45	chr12:46767132-46767182	GM12878	blood:	n/a
46	chr12:46767132-46767182	NB4	blood:	n/a
47	chr12:46767132-46767182	GM06990	blood:	n/a
48	chr12:46767132-46767182	HCT-116	colon:	n/a
49	chr12:46767132-46767182	GM12891	blood:	n/a
50	chr12:46767132-46767182	Jurkat	blood:	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:46656458..46664971-chr12:46763618..46767965,19	MCF-7	breast:
2	chr12:46652597..46666608-chr12:46757245..46767985,36	MCF-7	breast:
3	chr12:46766694..46767586-chr14:21945119..21945909,2	Hela-S3	cervix:
4	chr12:46381030..46386260-chr12:46762457..46768592,6	K562	blood:
5	chr12:46765603..46767339-chr12:49452531..49455344,2	K562	blood:
6	chr12:46658047..46664131-chr12:46762494..46767686,10	K562	blood:
7	chr12:46382586..46387481-chr12:46763277..46769922,9	K562	blood:
8	chr12:46767095..46767997-chr12:46777494..46778009,2	Hela-S3	cervix:
9	chr1:31538197..31538893-chr12:46766472..46767418,2	NB4	blood:
10	chr12:46766256..46767198-chr13:115046836..115047596,2	Hela-S3	cervix:
11	chr12:46765279..46767485-chr19:45580991..45583480,2	MCF-7	breast:
12	chr12:46767060..46767659-chr3:57582693..57583517,2	Hela-S3	cervix:

Variant related genes	Relation type
SLC38A2	TF binding region
SLC38A2	CpG island
ENSG00000139218	Chromatin interaction
ENSG00000272146	Chromatin interaction
ENSG00000111371	Chromatin interaction
ENSG00000092203	Chromatin interaction
ENSG00000007047	Chromatin interaction
ENSG00000168374	Chromatin interaction
ENSG00000142252	Chromatin interaction
ENSG00000167548	Chromatin interaction
ENSG00000257261	Chromatin interaction
ENSG00000169062	Chromatin interaction
ENSG00000129472	Chromatin interaction
ENSG00000134644	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10785620	0.86[EUR][1000 genomes]
rs10785624	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10785630	0.84[CHD][hapmap];0.80[JPT][hapmap];0.82[MEX][hapmap]
rs10880962	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs11183468	0.85[CEU][hapmap];0.81[CHB][hapmap]
rs12296120	0.87[EUR][1000 genomes]
rs12307969	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12320197	0.92[CEU][hapmap];0.90[TSI][hapmap];0.88[EUR][1000 genomes]
rs1873793	0.92[CEU][hapmap];0.90[TSI][hapmap];0.92[EUR][1000 genomes]
rs2408497	0.81[CEU][hapmap]
rs2897968	0.85[CEU][hapmap]
rs35377637	0.82[EUR][1000 genomes]
rs4076248	0.91[ASW][hapmap];0.85[CEU][hapmap];0.81[CHB][hapmap];0.98[CHD][hapmap];0.85[JPT][hapmap]
rs4768697	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs6582656	0.85[CEU][hapmap]
rs7487075	0.84[CEU][hapmap]
rs7979418	0.88[CEU][hapmap];0.81[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832398	chr12:46611692-46825530	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	181 gene(s)	inside rSNPs	diseases
2	esv1842882	chr12:46691487-47009428	Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	149 gene(s)	inside rSNPs	diseases
3	nsv1049525	chr12:46721742-47264172	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
4	nsv541486	chr12:46721742-47264172	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
5	esv3429861	chr12:46762813-46988789	Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	145 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	chr12:46762200-46767800	Active TSS	Right Ventricle	heart
2	chr12:46763400-46767400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr12:46763400-46767800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr12:46763600-46767600	Active TSS	Ovary	ovary
5	chr12:46763600-46767600	Active TSS	Psoas Muscle	Psoas
6	chr12:46763800-46767200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
7	chr12:46763800-46767200	Active TSS	Fetal Intestine Small	intestine
8	chr12:46764400-46767200	Active TSS	Rectal Mucosa Donor 31	rectum
9	chr12:46764400-46767600	Active TSS	Fetal Muscle Trunk	muscle
10	chr12:46764400-46767600	Active TSS	Small Intestine	intestine
11	chr12:46764400-46767600	Active TSS	HSMMtube	muscle
12	chr12:46764400-46767800	Bivalent/Poised TSS	HepG2	liver
13	chr12:46764400-46768000	Active TSS	Lung	lung
14	chr12:46764400-46768000	Active TSS	Rectal Smooth Muscle	rectum
15	chr12:46764600-46767400	Active TSS	Primary monocytes fromperipheralblood	blood
16	chr12:46764600-46767400	Active TSS	Duodenum Mucosa	Duodenum
17	chr12:46764600-46767400	Active TSS	Monocytes-CD14+_RO01746	blood
18	chr12:46764600-46767800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
19	chr12:46764600-46767800	Active TSS	Brain Anterior Caudate	brain
20	chr12:46764600-46767800	Active TSS	Colon Smooth Muscle	Colon
21	chr12:46764800-46767200	Active TSS	Fetal Brain Female	brain
22	chr12:46764800-46767400	Active TSS	Primary T cells from cord blood	blood
23	chr12:46764800-46767400	Active TSS	Pancreas	Pancrea
24	chr12:46764800-46767400	Active TSS	Spleen	Spleen
25	chr12:46764800-46767600	Active TSS	Primary T killer memory cells from peripheral blood	blood
26	chr12:46764800-46767600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr12:46764800-46767600	Active TSS	Brain Substantia Nigra	brain
28	chr12:46764800-46767600	Active TSS	Pancreatic Islets	Pancreatic Islet
29	chr12:46764800-46767600	Active TSS	Gastric	stomach
30	chr12:46765000-46767200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr12:46765000-46767200	Active TSS	Placenta	Placenta
32	chr12:46765000-46767200	Active TSS	GM12878-XiMat	blood
33	chr12:46765000-46767400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr12:46765000-46767400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr12:46765000-46767400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr12:46765000-46767400	Active TSS	Primary B cells from peripheral blood	blood
37	chr12:46765000-46767400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
38	chr12:46765000-46767600	Active TSS	Brain Angular Gyrus	brain
39	chr12:46765000-46767600	Active TSS	NHDF-Ad	bronchial
40	chr12:46765000-46767800	Active TSS	Brain Cingulate Gyrus	brain
41	chr12:46765000-46767800	Active TSS	Stomach Mucosa	stomach
42	chr12:46765200-46767200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
43	chr12:46765200-46767200	Active TSS	Primary T helper cells PMA-I stimulated	--
44	chr12:46765200-46767200	Active TSS	Skeletal Muscle Female	skeletal muscle
45	chr12:46765200-46767400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr12:46765200-46767400	Active TSS	HUES48 Cell Line	embryonic stem cell
47	chr12:46765200-46767400	Active TSS	HUES64 Cell Line	embryonic stem cell
48	chr12:46765200-46767400	Active TSS	iPS-18 Cell Line	embryonic stem cell
49	chr12:46765200-46767400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr12:46765200-46767400	Active TSS	Breast Myoepithelial Primary Cells	Breast

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