Variant report

Variant	rs13390828
Chromosome Location	chr2:152955805-152955806
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:38)
CpG islands
(count:122)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:38 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:152955113-152956382	GM12891	blood:	n/a	n/a
2	CTBP2	chr2:152955151-152956076	H1-hESC	embryonic stem cell:	n/a	n/a
3	MYC	chr2:152955390-152956237	NB4	blood:	n/a	n/a
4	TCF7L2	chr2:152955314-152956100	HCT-116	colon:	n/a	n/a
5	HDAC2	chr2:152955489-152955843	H1-hESC	embryonic stem cell:	n/a	chr2:152955714-152955723
6	MAX	chr2:152955107-152956178	H1-hESC	embryonic stem cell:	n/a	n/a
7	MAX	chr2:152955165-152956303	ECC-1	luminal epithelium:	n/a	n/a
8	PML	chr2:152955406-152956315	GM12878	blood:	n/a	n/a
9	MAX	chr2:152955125-152956244	A549	lung:	n/a	n/a
10	E2F6	chr2:152955255-152956000	H1-hESC	embryonic stem cell:	n/a	chr2:152955643-152955652 chr2:152955641-152955650
11	ZBTB7A	chr2:152955067-152956024	ECC-1	luminal epithelium:	n/a	n/a
12	SUZ12	chr2:152953899-152956422	NT2-D1	testis:	n/a	n/a
13	ZNF263	chr2:152953867-152956292	HEK293-T-REx	kidney:	n/a	chr2:152955418-152955439 chr2:152954806-152954815
14	BACH1	chr2:152955561-152955889	H1-hESC	embryonic stem cell:	n/a	n/a
15	MAX	chr2:152955223-152956093	A549	lung:	n/a	n/a
16	KAP1	chr2:152955700-152956417	HEK293	kidney:	n/a	n/a
17	MTA3	chr2:152954766-152956281	GM12878	blood:	n/a	n/a
18	MAX	chr2:152955382-152956171	H1-hESC	embryonic stem cell:	n/a	n/a
19	NFIC	chr2:152955102-152955893	GM12878	blood:	n/a	n/a
20	TCF12	chr2:152955104-152955884	ECC-1	luminal epithelium:	n/a	n/a
21	MAX	chr2:152955360-152956251	NB4	blood:	n/a	n/a
22	POLR2A	chr2:152955057-152956502	H1-neurons	neurons:	n/a	n/a
23	RUNX3	chr2:152955764-152956306	GM12878	blood:	n/a	n/a
24	SIN3A	chr2:152955472-152956205	H1-hESC	embryonic stem cell:	n/a	n/a
25	ZNF143	chr2:152955242-152956328	H1-hESC	embryonic stem cell:	n/a	chr2:152955640-152955650
26	TCF7L2	chr2:152955682-152955882	PANC-1	pancreas:	n/a	n/a
27	ELF1	chr2:152955274-152955820	GM12878	blood:	n/a	chr2:152955557-152955569
28	MAX	chr2:152955131-152956215	ECC-1	luminal epithelium:	n/a	n/a
29	POLR2A	chr2:152955161-152956273	GM12892	blood:	n/a	n/a
30	POLR2A	chr2:152955134-152956169	GM19193	blood:	n/a	n/a
31	POLR2A	chr2:152955128-152956062	GM18951	blood:	n/a	n/a
32	POLR2A	chr2:152954483-152956221	GM12892	blood:	n/a	n/a
33	MAX	chr2:152955179-152955838	H1-hESC	embryonic stem cell:	n/a	n/a
34	POLR2A	chr2:152955092-152956850	H1-neurons	neurons:	n/a	n/a
35	REST	chr2:152955053-152956273	H1-neurons	neurons:	n/a	chr2:152956116-152956136 chr2:152955557-152955570 chr2:152955664-152955684 chr2:152955537-152955550 chr2:152955594-152955607
36	ZBTB7A	chr2:152955002-152956182	ECC-1	luminal epithelium:	n/a	n/a
37	ELF1	chr2:152954508-152956241	GM12878	blood:	n/a	chr2:152955557-152955569 chr2:152955218-152955230
38	E2F6	chr2:152954439-152956260	H1-hESC	embryonic stem cell:	n/a	chr2:152955643-152955652 chr2:152956200-152956208 chr2:152956200-152956208 chr2:152955641-152955650 chr2:152956199-152956209 chr2:152954822-152954834 chr2:152956201-152956208

(count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr2:152955765-152955815	BJ	skin:	n/a
2	chr2:152955765-152955815	PrEC	prostate:	n/a
3	chr2:152955765-152955815	HNPCEpiC	eye:	n/a
4	chr2:152955765-152955815	HCF	heart:	n/a
5	chr2:152955783-152955833	Jurkat	blood:	n/a
6	chr2:152955783-152955833	GM12891	blood:	n/a
7	chr2:152955765-152955815	HIPEpiC	eye:	n/a
8	chr2:152955783-152955833	MCF10A-Er-Src	breast:	n/a
9	chr2:152955783-152955833	NB4	blood:	n/a
10	chr2:152955783-152955833	HRPEpiC	eye:	n/a
11	chr2:152955765-152955815	HEK293	kidney:	embryo
12	chr2:152955783-152955833	HCF	heart:	n/a
13	chr2:152955783-152955833	HMEC	breast:	n/a
14	chr2:152955783-152955833	AoSMC	blood vessel:	n/a
15	chr2:152955765-152955815	PFSK-1	brain:	n/a
16	chr2:152955765-152955815	HRE	kidney:	n/a
17	chr2:152955765-152955815	MCF10A-Er-Src	breast:	n/a
18	chr2:152955765-152955815	HEEpiC	esophagus:	n/a
19	chr2:152955783-152955833	SKMC	muscle:	n/a
20	chr2:152955765-152955815	HRCEpiC	kidney:	n/a
21	chr2:152955783-152955833	U87	brain:	n/a
22	chr2:152955783-152955833	HRCEpiC	kidney:	n/a
23	chr2:152955765-152955815	HUVEC	blood vessel:	n/a
24	chr2:152955783-152955833	HCT-116	colon:	n/a
25	chr2:152955783-152955833	RPTEC	kidney:	n/a
26	chr2:152955783-152955833	BJ	skin:	n/a
27	chr2:152955765-152955815	AG09309	skin:	n/a
28	chr2:152955765-152955815	HMEC	breast:	n/a
29	chr2:152955765-152955815	SAEC	small airway:	n/a
30	chr2:152955783-152955833	AG04450	lung:	fetal
31	chr2:152955765-152955815	Hela-S3	cervix:	n/a
32	chr2:152955765-152955815	HCPEpiC	choroid plexus:	n/a
33	chr2:152955765-152955815	ProgFib	skin:	n/a
34	chr2:152955765-152955815	HCT-116	colon:	n/a
35	chr2:152955765-152955815	GM19239	blood:	n/a
36	chr2:152955783-152955833	NHBE	bronchial:	n/a
37	chr2:152955765-152955815	CMK	blood:	n/a
38	chr2:152955783-152955833	HL-60	blood:	n/a
39	chr2:152955783-152955833	HIPEpiC	eye:	n/a
40	chr2:152955765-152955815	Jurkat	blood:	n/a
41	chr2:152955783-152955833	HEK293	kidney:	embryo
42	chr2:152955783-152955833	BE2_C	brain:	n/a
43	chr2:152955765-152955815	HPAEpiC	pulmonary alveolar:	n/a
44	chr2:152955765-152955815	HCM	heart:	n/a
45	chr2:152955783-152955833	HEEpiC	esophagus:	n/a
46	chr2:152955783-152955833	PANC-1	pancreas:	n/a
47	chr2:152955783-152955833	T-47D	breast:	n/a
48	chr2:152955765-152955815	U87	brain:	n/a
49	chr2:152955765-152955815	H1-hESC	embryonic stem cell:	embryo
50	chr2:152955783-152955833	SK-N-SH	brain:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:152954463..152956019-chr2:153031201..153033706,2	MCF-7	breast:

No data

Variant related genes	Relation type
CACNB4	TF binding region
CACNB4	CpG island
ENSG00000115145	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10166701	1.00[CHB][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.95[YRI][hapmap];1.00[ASN][1000 genomes]
rs10181910	1.00[ASN][1000 genomes]
rs10188437	1.00[ASN][1000 genomes]
rs10190828	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10202920	1.00[CHB][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.95[YRI][hapmap];0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10203589	1.00[CHB][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.95[YRI][hapmap];0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10209826	1.00[CHB][hapmap];0.95[YRI][hapmap];0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11678763	1.00[CHD][hapmap]
rs12693278	1.00[CHB][hapmap];0.85[YRI][hapmap];1.00[ASN][1000 genomes]
rs13382381	1.00[CHB][hapmap];0.95[YRI][hapmap];1.00[ASN][1000 genomes]
rs13386095	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs13390486	1.00[ASW][hapmap];1.00[GIH][hapmap];0.84[LWK][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13394982	1.00[ASN][1000 genomes]
rs13408535	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13408915	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13415898	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13416727	1.00[CEU][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13420003	1.00[ASN][1000 genomes]
rs16830583	1.00[MEX][hapmap]
rs28581765	1.00[ASN][1000 genomes]
rs35406869	1.00[ASN][1000 genomes]
rs58932175	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs59794582	1.00[ASN][1000 genomes]
rs6726207	1.00[ASN][1000 genomes]
rs6742020	1.00[ASN][1000 genomes]
rs6742139	1.00[ASN][1000 genomes]
rs6753703	1.00[CHB][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.95[YRI][hapmap];1.00[ASN][1000 genomes]
rs7590270	1.00[ASN][1000 genomes]
rs7600978	1.00[ASN][1000 genomes]
rs7604840	1.00[ASN][1000 genomes]
rs9288079	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005746	chr2:152361972-153059840	Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv535984	chr2:152361972-153059840	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	esv3693431	chr2:152683731-152981827	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv875287	chr2:152714680-153110573	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	nsv875288	chr2:152716628-153183646	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
6	nsv875289	chr2:152720030-153183646	Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
7	esv1847028	chr2:152863856-153045036	Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13390828	KRT18	trans	lymphoblastoid	seeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:152953200-152956000	Active TSS	Brain Anterior Caudate	brain
2	chr2:152953600-152956200	Active TSS	Brain Angular Gyrus	brain
3	chr2:152953800-152956000	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
4	chr2:152953800-152956200	Active TSS	Breast Myoepithelial Primary Cells	Breast
5	chr2:152953800-152956400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
6	chr2:152953800-152956400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
7	chr2:152954000-152956000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr2:152954000-152956000	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr2:152954000-152956000	Active TSS	Esophagus	oesophagus
10	chr2:152954000-152956000	Active TSS	Pancreatic Islets	Pancreatic Islet
11	chr2:152954000-152956200	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
12	chr2:152954000-152956200	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr2:152954200-152956000	Bivalent/Poised TSS	Fetal Intestine Large	intestine
14	chr2:152954200-152956000	Active TSS	Gastric	stomach
15	chr2:152954200-152956000	Active TSS	Lung	lung
16	chr2:152954200-152956000	Active TSS	Pancreas	Pancrea
17	chr2:152954200-152956000	Active TSS	Right Ventricle	heart
18	chr2:152954200-152956000	Bivalent/Poised TSS	A549	lung
19	chr2:152954200-152956200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
20	chr2:152954200-152956200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
21	chr2:152954200-152956400	Active TSS	Right Atrium	heart
22	chr2:152954400-152956000	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr2:152954400-152956000	Flanking Active TSS	Primary hematopoietic stem cells	blood
24	chr2:152954400-152956000	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr2:152954400-152956000	Active TSS	Brain Substantia Nigra	brain
26	chr2:152954400-152956000	Bivalent/Poised TSS	Thymus	Thymus
27	chr2:152954400-152956200	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr2:152954400-152956200	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr2:152954400-152956200	Active TSS	Fetal Kidney	kidney
30	chr2:152954400-152956200	Flanking Active TSS	Stomach Smooth Muscle	stomach
31	chr2:152954400-152956400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
32	chr2:152954600-152956000	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr2:152954600-152956000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr2:152954600-152956000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
35	chr2:152954600-152956000	Flanking Bivalent TSS/Enh	HMEC	breast
36	chr2:152954600-152956200	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr2:152954600-152956200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
38	chr2:152954600-152956200	Bivalent/Poised TSS	ES-UCSF4 Cell Line	embryonic stem cell
39	chr2:152954600-152956200	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr2:152954600-152956200	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
41	chr2:152954600-152956400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
42	chr2:152954800-152956000	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
43	chr2:152954800-152956200	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
44	chr2:152954800-152956400	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr2:152954800-152956600	Active TSS	Fetal Brain Female	brain
46	chr2:152955000-152956000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr2:152955000-152956000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr2:152955000-152956000	Active TSS	Brain Inferior Temporal Lobe	brain
49	chr2:152955000-152956400	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
50	chr2:152955000-152956400	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon

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