Variant report

Variant	rs13412879
Chromosome Location	chr2:191399378-191399379
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:428)
CpG islands
(count:61)
Chromatin interactive
region (count:10)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:428 , 50 per page) page: 1 2 3 4 5 6 7 ... 9

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TAF1	chr2:191398998-191399616	K562	blood:	n/a	n/a
2	POLR2A	chr2:191398432-191399945	GM12892	blood:	n/a	n/a
3	CREB1	chr2:191398487-191400032	HepG2	liver:	n/a	n/a
4	FOXM1	chr2:191398636-191399767	GM12878	blood:	n/a	n/a
5	CHD1	chr2:191399373-191399642	H1-hESC	embryonic stem cell:	n/a	n/a
6	RCOR1	chr2:191398537-191399781	HepG2	liver:	n/a	n/a
7	TAF1	chr2:191398951-191399743	SK-N-SH	brain:	n/a	n/a
8	POLR2A	chr2:191398588-191399893	GM10847	blood:	n/a	n/a
9	GABPA	chr2:191399107-191399864	K562	blood:	n/a	chr2:191399124-191399133 chr2:191399556-191399565
10	MYC	chr2:191399211-191399428	GM12878	blood:	n/a	n/a
11	HNF4G	chr2:191398550-191399862	HepG2	liver:	n/a	chr2:191399384-191399400
12	POLR2A	chr2:191398552-191400035	PBDE	blood:	n/a	n/a
13	HEY1	chr2:191399009-191399909	K562	blood:	n/a	n/a
14	MYC	chr2:191399200-191399735	HepG2	liver:	n/a	chr2:191399561-191399571
15	RCOR1	chr2:191398572-191399754	K562	blood:	n/a	n/a
16	CTBP2	chr2:191398908-191399893	H1-hESC	embryonic stem cell:	n/a	n/a
17	POLR2A	chr2:191398838-191399912	HCT-116	colon:	n/a	n/a
18	TAF1	chr2:191399107-191399786	A549	lung:	n/a	n/a
19	USF2	chr2:191398237-191399549	GM12878	blood:	n/a	chr2:191398742-191398753
20	POLR2A	chr2:191398519-191399978	HepG2	liver:	n/a	n/a
21	POLR2A	chr2:191398983-191399850	A549	lung:	n/a	n/a
22	POLR2A	chr2:191399033-191399749	K562	blood:	n/a	n/a
23	ELF1	chr2:191399054-191399846	K562	blood:	n/a	chr2:191399562-191399574 chr2:191399469-191399481
24	POLR2A	chr2:191398856-191399903	Hela-S3	cervix:	n/a	n/a
25	TCF12	chr2:191398962-191399996	ECC-1	luminal epithelium:	n/a	n/a
26	POLR2A	chr2:191398912-191399898	ECC-1	luminal epithelium:	n/a	n/a
27	SMARCB1	chr2:191398560-191399879	Hela-S3	cervix:	n/a	n/a
28	POLR2A	chr2:191399044-191399882	H1-hESC	embryonic stem cell:	n/a	n/a
29	YY1	chr2:191399355-191399669	HCT-116	colon:	n/a	chr2:191399468-191399477 chr2:191399560-191399574 chr2:191399554-191399568
30	RFX5	chr2:191398752-191400077	Hela-S3	cervix:	n/a	n/a
31	MAX	chr2:191398589-191400113	A549	lung:	n/a	chr2:191399561-191399571
32	POLR2A	chr2:191398963-191399787	IMR90	lung:	n/a	n/a
33	PBX3	chr2:191399101-191400128	SK-N-SH	brain:	n/a	chr2:191399849-191399858
34	E2F6	chr2:191398980-191399885	K562	blood:	n/a	chr2:191399494-191399501 chr2:191399204-191399218 chr2:191399207-191399221 chr2:191399494-191399501 chr2:191399124-191399133 chr2:191399128-191399138 chr2:191399490-191399502 chr2:191399494-191399501 chr2:191399510-191399519
35	TAF1	chr2:191399022-191399526	PFSK-1	brain:	n/a	n/a
36	RCOR1	chr2:191398561-191399842	GM12878	blood:	n/a	n/a
37	JUND	chr2:191399091-191399679	HepG2	liver:	n/a	chr2:191399511-191399520 chr2:191399123-191399132
38	POLR2A	chr2:191398545-191399782	HepG2	liver:	n/a	n/a
39	POLR2A	chr2:191398800-191399773	K562	blood:	n/a	n/a
40	CHD2	chr2:191398899-191399855	Hela-S3	cervix:	n/a	n/a
41	REST	chr2:191398982-191399713	H1-neurons	neurons:	n/a	chr2:191399426-191399446 chr2:191399548-191399561
42	POLR2A	chr2:191398351-191399847	GM12878	blood:	n/a	n/a
43	POLR2A	chr2:191399048-191399784	A549	lung:	n/a	n/a
44	YY1	chr2:191398501-191399822	GM12891	blood:	n/a	chr2:191399468-191399477 chr2:191399560-191399574 chr2:191399554-191399568
45	TAF1	chr2:191399049-191399749	HepG2	liver:	n/a	n/a
46	POLR2A	chr2:191398872-191399907	K562	blood:	n/a	n/a
47	YY1	chr2:191398937-191399873	HepG2	liver:	n/a	chr2:191399468-191399477 chr2:191399560-191399574 chr2:191399554-191399568
48	MAX	chr2:191398480-191400024	MCF-7	breast:	n/a	chr2:191399561-191399571
49	EP300	chr2:191399085-191399722	H1-hESC	embryonic stem cell:	n/a	chr2:191399551-191399567
50	MYC	chr2:191399124-191399754	MCF-7	breast:	n/a	chr2:191399561-191399571

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr2:191399337-191399387	HRE	kidney:	n/a
2	chr2:191399337-191399387	Jurkat	blood:	n/a
3	chr2:191399337-191399387	HUVEC	blood vessel:	n/a
4	chr2:191399337-191399387	MCF10A-Er-Src	breast:	n/a
5	chr2:191399337-191399387	NT2-D1	testis:	n/a
6	chr2:191399337-191399387	ECC-1	luminal epithelium:	n/a
7	chr2:191399337-191399387	HepG2	liver:	n/a
8	chr2:191399337-191399387	AG04450	lung:	fetal
9	chr2:191399337-191399387	HCF	heart:	n/a
10	chr2:191399337-191399387	GM12891	blood:	n/a
11	chr2:191399337-191399387	LNCaP	prostate:	n/a
12	chr2:191399337-191399387	H1-hESC	embryonic stem cell:	embryo
13	chr2:191399337-191399387	BJ	skin:	n/a
14	chr2:191399337-191399387	K562	blood:	n/a
15	chr2:191399337-191399387	GM19239	blood:	n/a
16	chr2:191399337-191399387	AG10803	skin:	n/a
17	chr2:191399337-191399387	AoSMC	blood vessel:	n/a
18	chr2:191399337-191399387	A549	lung:	n/a
19	chr2:191399337-191399387	U87	brain:	n/a
20	chr2:191399337-191399387	Hela-S3	cervix:	n/a
21	chr2:191399337-191399387	Hepatocyte	liver:	n/a
22	chr2:191399337-191399387	HEK293	kidney:	embryo
23	chr2:191399337-191399387	ProgFib	skin:	n/a
24	chr2:191399337-191399387	NHDF-neo	bronchial:	n/a
25	chr2:191399337-191399387	HRPEpiC	eye:	n/a
26	chr2:191399337-191399387	HIPEpiC	eye:	n/a
27	chr2:191399337-191399387	HPAEpiC	pulmonary alveolar:	n/a
28	chr2:191399337-191399387	HRCEpiC	kidney:	n/a
29	chr2:191399337-191399387	NB4	blood:	n/a
30	chr2:191399337-191399387	HMEC	breast:	n/a
31	chr2:191399337-191399387	PFSK-1	brain:	n/a
32	chr2:191399337-191399387	GM12878	blood:	n/a
33	chr2:191399337-191399387	GM12892	blood:	n/a
34	chr2:191399337-191399387	SK-N-SH_RA	brain:	n/a
35	chr2:191399337-191399387	HCT-116	colon:	n/a
36	chr2:191399337-191399387	HCM	heart:	n/a
37	chr2:191399337-191399387	BE2_C	brain:	n/a
38	chr2:191399337-191399387	HCPEpiC	choroid plexus:	n/a
39	chr2:191399337-191399387	HNPCEpiC	eye:	n/a
40	chr2:191399337-191399387	SK-N-MC	brain:	n/a
41	chr2:191399337-191399387	PrEC	prostate:	n/a
42	chr2:191399337-191399387	ovcar-3	ovarian:	n/a
43	chr2:191399337-191399387	RPTEC	kidney:	n/a
44	chr2:191399337-191399387	AG04449	skin:	fetal
45	chr2:191399337-191399387	T-47D	breast:	n/a
46	chr2:191399337-191399387	HEEpiC	esophagus:	n/a
47	chr2:191399337-191399387	AG09309	skin:	n/a
48	chr2:191399337-191399387	GM06990	blood:	n/a
49	chr2:191399337-191399387	Caco-2	colon:	n/a
50	chr2:191399337-191399387	SAEC	small airway:	n/a

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:191397602..191400323-chr2:191511853..191515845,7	MCF-7	breast:
2	chr2:191398826..191399506-chr5:43483586..43484093,2	Hela-S3	cervix:
3	chr2:191398910..191400669-chr2:191512631..191515436,2	K562	blood:
4	chr17:56735377..56737790-chr2:191398631..191400181,2	MCF-7	breast:
5	chr2:191397324..191399612-chr2:191415383..191418342,2	MCF-7	breast:
6	chr2:191397736..191401145-chr2:191512338..191515436,3	K562	blood:
7	chr2:191271812..191274120-chr2:191398223..191400840,2	K562	blood:
8	chr2:191389345..191393382-chr2:191397304..191400533,4	MCF-7	breast:
9	chr11:62608608..62609474-chr2:191399064..191400024,3	Hela-S3	cervix:
10	chr12:27933434..27934346-chr2:191398826..191399467,2	Hela-S3	cervix:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MFSD6-1	chr2:191399293-191399847	NONHSAT076087
2	lnc-MFSD6-1	chr2:191399293-191399847	NONHSAT076088

No data

Variant related genes	Relation type
ENSG00000233654	TF binding region
TMEM194B	TF binding region
TMEM194B	CpG island
ENSG00000233654	CpG island
ENSG00000151881	Chromatin interaction
ENSG00000138386	Chromatin interaction
ENSG00000251935	Chromatin interaction
ENSG00000189362	Chromatin interaction
ENSG00000087448	Chromatin interaction
ENSG00000256747	Chromatin interaction
ENSG00000151690	Chromatin interaction
ENSG00000133316	Chromatin interaction
ENSG00000202077	Chromatin interaction
ENSG00000249492	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10169169	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10171376	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10173975	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10179262	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10185147	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10189140	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10202274	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10204342	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10208737	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10209340	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10211375	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11553601	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13031452	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13384743	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13386210	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13388162	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13395233	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13398741	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13405215	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13410179	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13412663	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13412823	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13412835	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13417310	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13418943	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13429315	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3811608	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4283453	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4853712	0.86[ASN][1000 genomes]
rs58210597	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58253207	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58433478	0.84[ASN][1000 genomes]
rs6717050	0.89[ASN][1000 genomes]
rs72905242	0.84[ASN][1000 genomes]
rs73054092	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7556716	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7560045	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7562013	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7564107	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7574844	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7584379	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7594994	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7609330	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9288174	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs13412879	NAB1	cis	Esophagus Mucosa	GTEx
rs13412879	NAB1	Cis_1M	lymphoblastoid	RTeQTL
rs13412879	FLJ20160	cis	multi-tissue	Pritchard
rs13412879	FLJ20160	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:191397800-191401000	Active TSS	Duodenum Smooth Muscle	Duodenum
2	chr2:191398000-191401000	Active TSS	GM12878-XiMat	blood
3	chr2:191398200-191400000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr2:191398200-191400000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
5	chr2:191398200-191401200	Flanking Active TSS	Primary hematopoietic stem cells	blood
6	chr2:191398400-191399800	Flanking Active TSS	HMEC	breast
7	chr2:191398400-191400000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
8	chr2:191398400-191400000	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
9	chr2:191398400-191400000	Active TSS	Lung	lung
10	chr2:191398400-191400200	Active TSS	Psoas Muscle	Psoas
11	chr2:191398400-191400400	Active TSS	Aorta	Aorta
12	chr2:191398400-191400600	Active TSS	Pancreatic Islets	Pancreatic Islet
13	chr2:191398600-191399600	Active TSS	Primary T helper cells PMA-I stimulated	--
14	chr2:191398600-191400000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr2:191398600-191400000	Active TSS	Esophagus	oesophagus
16	chr2:191398600-191400000	Active TSS	Ovary	ovary
17	chr2:191398600-191400400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr2:191398800-191399800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr2:191398800-191399800	Active TSS	Primary T cells from cord blood	blood
20	chr2:191398800-191399800	Active TSS	Small Intestine	intestine
21	chr2:191398800-191399800	Active TSS	Spleen	Spleen
22	chr2:191398800-191400000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr2:191398800-191400000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr2:191398800-191400000	Active TSS	Brain Angular Gyrus	brain
25	chr2:191398800-191400000	Active TSS	Gastric	stomach
26	chr2:191398800-191400000	Active TSS	Left Ventricle	heart
27	chr2:191398800-191400000	Active TSS	Pancreas	Pancrea
28	chr2:191398800-191400000	Active TSS	Sigmoid Colon	Sigmoid Colon
29	chr2:191398800-191400200	Active TSS	Primary hematopoietic stem cells short term culture	blood
30	chr2:191398800-191400200	Active TSS	Primary T helper naive cells from peripheral blood	blood
31	chr2:191398800-191400200	Active TSS	Primary T killer naive cells fromperipheralblood	blood
32	chr2:191398800-191400200	Active TSS	Brain Anterior Caudate	brain
33	chr2:191398800-191400200	Active TSS	Brain Substantia Nigra	brain
34	chr2:191398800-191400200	Active TSS	Duodenum Mucosa	Duodenum
35	chr2:191398800-191400200	Active TSS	Fetal Lung	lung
36	chr2:191398800-191400200	Active TSS	Placenta	Placenta
37	chr2:191398800-191400200	Active TSS	Rectal Mucosa Donor 29	rectum
38	chr2:191398800-191400200	Active TSS	Skeletal Muscle Male	skeletal muscle
39	chr2:191398800-191400400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr2:191398800-191400400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr2:191398800-191400400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
42	chr2:191398800-191400400	Active TSS	Stomach Smooth Muscle	stomach
43	chr2:191398800-191400400	Active TSS	Thymus	Thymus
44	chr2:191398800-191400600	Active TSS	ES-I3 Cell Line	embryonic stem cell
45	chr2:191398800-191400600	Active TSS	Breast Myoepithelial Primary Cells	Breast
46	chr2:191398800-191400600	Active TSS	Primary T killer memory cells from peripheral blood	blood
47	chr2:191398800-191400600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr2:191398800-191400600	Active TSS	Colon Smooth Muscle	Colon
49	chr2:191398800-191400600	Active TSS	Fetal Intestine Small	intestine
50	chr2:191398800-191400600	Active TSS	Fetal Kidney	kidney

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