Variant report

Variant	rs9945420
Chromosome Location	chr18:29078516-29078517
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	TAF1	chr18:29078416-29078630	GM12892	blood:	n/a	n/a
2	YY1	chr18:29077681-29078582	K562	blood:	n/a	chr18:29078340-29078349 chr18:29078403-29078417 chr18:29077999-29078011
3	MXI1	chr18:29078411-29078816	K562	blood:	n/a	n/a
4	TBL1XR1	chr18:29077623-29078707	K562	blood:	n/a	n/a
5	MAX	chr18:29077454-29078702	K562	blood:	n/a	n/a
6	MAX	chr18:29077372-29078768	K562	blood:	n/a	n/a
7	POLR2A	chr18:29077478-29078590	HCT-116	colon:	n/a	n/a
8	SIN3A	chr18:29078123-29078628	GM12878	blood:	n/a	n/a
9	ELF1	chr18:29077711-29078655	GM12878	blood:	n/a	n/a
10	ZMIZ1	chr18:29077670-29078830	K562	blood:	n/a	n/a
11	MAX	chr18:29077944-29078631	HepG2	liver:	n/a	n/a
12	CHD2	chr18:29077693-29078755	GM12878	blood:	n/a	chr18:29077809-29077819 chr18:29078035-29078042
13	RFX5	chr18:29078478-29078678	GM12878	blood:	n/a	n/a
14	POLR2A	chr18:29077752-29078720	K562	blood:	n/a	n/a
15	HA-E2F1	chr18:29077751-29078624	Hela-S3	cervix:	n/a	chr18:29078340-29078349 chr18:29078035-29078042 chr18:29077940-29077949 chr18:29077862-29077872
16	SMC3	chr18:29077842-29078734	Hela-S3	cervix:	n/a	n/a
17	MAX	chr18:29077794-29078696	ECC-1	luminal epithelium:	n/a	n/a
18	RFX5	chr18:29078126-29078609	Hela-S3	cervix:	n/a	n/a
19	PML	chr18:29077777-29078555	GM12878	blood:	n/a	n/a
20	E2F4	chr18:29077961-29078670	MCF10A-Er-Src	breast:	n/a	chr18:29078006-29078017 chr18:29078340-29078349 chr18:29078035-29078042
21	POLR2A	chr18:29077385-29078758	H1-hESC	embryonic stem cell:	n/a	n/a
22	POLR2A	chr18:29077369-29078739	H1-hESC	embryonic stem cell:	n/a	n/a
23	MAX	chr18:29077838-29078718	A549	lung:	n/a	n/a
24	POLR2A	chr18:29078084-29078838	GM12878	blood:	n/a	n/a
25	TAF1	chr18:29077667-29078669	ECC-1	luminal epithelium:	n/a	n/a
26	E2F6	chr18:29077496-29078610	K562	blood:	n/a	chr18:29077690-29077700 chr18:29078340-29078349 chr18:29078035-29078042 chr18:29077940-29077949 chr18:29077862-29077872
27	POLR2A	chr18:29077620-29078715	K562	blood:	n/a	n/a
28	YY1	chr18:29077517-29078685	K562	blood:	n/a	chr18:29078340-29078349 chr18:29078403-29078417 chr18:29077999-29078011
29	POLR2A	chr18:29077487-29078653	HepG2	liver:	n/a	n/a
30	MAX	chr18:29077944-29078760	Hela-S3	cervix:	n/a	n/a
31	RAD21	chr18:29078408-29078636	H1-hESC	embryonic stem cell:	n/a	n/a
32	TFAP2C	chr18:29077718-29078777	Hela-S3	cervix:	n/a	chr18:29078083-29078098
33	GTF2F1	chr18:29078317-29078806	Hela-S3	cervix:	n/a	n/a
34	YY1	chr18:29077655-29078718	GM12878	blood:	n/a	chr18:29078340-29078349 chr18:29078403-29078417 chr18:29077999-29078011
35	STAT1	chr18:29078143-29078549	GM12878	blood:	n/a	n/a
36	JUND	chr18:29077322-29078758	K562	blood:	n/a	chr18:29077857-29077866
37	TAF7	chr18:29077349-29078695	H1-hESC	embryonic stem cell:	n/a	n/a
38	POLR2A	chr18:29077812-29078578	Hela-S3	cervix:	n/a	n/a
39	YY1	chr18:29077471-29078581	HepG2	liver:	n/a	chr18:29078340-29078349 chr18:29078403-29078417 chr18:29077999-29078011
40	POLR2A	chr18:29077557-29078773	GM19193	blood:	n/a	n/a
41	POLR2A	chr18:29077558-29078683	GM12878	blood:	n/a	n/a
42	HEY1	chr18:29078100-29078769	K562	blood:	n/a	n/a
43	POLR2A	chr18:29077587-29078727	GM12892	blood:	n/a	n/a
44	YY1	chr18:29077694-29078635	GM12891	blood:	n/a	chr18:29078340-29078349 chr18:29078403-29078417 chr18:29077999-29078011
45	EGR1	chr18:29078455-29078648	GM12878	blood:	n/a	chr18:29078539-29078553 chr18:29078539-29078550
46	POLR2A	chr18:29077611-29079895	K562	blood:	n/a	n/a
47	E2F6	chr18:29077478-29078605	K562	blood:	n/a	chr18:29077690-29077700 chr18:29078340-29078349 chr18:29078035-29078042 chr18:29077940-29077949 chr18:29077862-29077872
48	UBTF	chr18:29077381-29078714	K562	blood:	n/a	n/a
49	RUNX3	chr18:29077873-29078676	GM12878	blood:	n/a	n/a
50	ZC3H11A	chr18:29078451-29078642	K562	blood:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr18:29078478-29078528	A549	lung:	n/a
2	chr18:29078478-29078528	HEEpiC	esophagus:	n/a
3	chr18:29078478-29078528	SAEC	small airway:	n/a
4	chr18:29078478-29078528	BE2_C	brain:	n/a
5	chr18:29078478-29078528	HNPCEpiC	eye:	n/a
6	chr18:29078478-29078528	HCT-116	colon:	n/a
7	chr18:29078478-29078528	IMR90	lung:	fetal
8	chr18:29078478-29078528	NHBE	bronchial:	n/a
9	chr18:29078478-29078528	HRPEpiC	eye:	n/a
10	chr18:29078478-29078528	SKMC	muscle:	n/a
11	chr18:29078478-29078528	NT2-D1	testis:	n/a
12	chr18:29078478-29078528	ECC-1	luminal epithelium:	n/a
13	chr18:29078478-29078528	HCF	heart:	n/a
14	chr18:29078478-29078528	GM12878	blood:	n/a
15	chr18:29078478-29078528	ProgFib	skin:	n/a
16	chr18:29078478-29078528	HUVEC	blood vessel:	n/a
17	chr18:29078478-29078528	AG04450	lung:	fetal
18	chr18:29078478-29078528	AG10803	skin:	n/a
19	chr18:29078478-29078528	HRE	kidney:	n/a
20	chr18:29078478-29078528	HPAEpiC	pulmonary alveolar:	n/a
21	chr18:29078478-29078528	HepG2	liver:	n/a
22	chr18:29078478-29078528	LNCaP	prostate:	n/a
23	chr18:29078478-29078528	Hepatocyte	liver:	n/a
24	chr18:29078478-29078528	Hela-S3	cervix:	n/a
25	chr18:29078478-29078528	MCF-7	breast:	n/a
26	chr18:29078478-29078528	PFSK-1	brain:	n/a
27	chr18:29078478-29078528	U87	brain:	n/a
28	chr18:29078478-29078528	HEK293	kidney:	embryo
29	chr18:29078478-29078528	PANC-1	pancreas:	n/a
30	chr18:29078478-29078528	SK-N-SH_RA	brain:	n/a
31	chr18:29078478-29078528	NHDF-neo	bronchial:	n/a
32	chr18:29078478-29078528	SK-N-SH	brain:	n/a
33	chr18:29078478-29078528	HIPEpiC	eye:	n/a
34	chr18:29078478-29078528	PrEC	prostate:	n/a
35	chr18:29078478-29078528	SK-N-MC	brain:	n/a
36	chr18:29078478-29078528	HAEpiC	amniotic membrane:	n/a
37	chr18:29078478-29078528	HL-60	blood:	n/a
38	chr18:29078478-29078528	ovcar-3	ovarian:	n/a
39	chr18:29078478-29078528	AoSMC	blood vessel:	n/a
40	chr18:29078478-29078528	RPTEC	kidney:	n/a
41	chr18:29078478-29078528	Jurkat	blood:	n/a
42	chr18:29078478-29078528	GM12892	blood:	n/a
43	chr18:29078478-29078528	H1-hESC	embryonic stem cell:	embryo
44	chr18:29078478-29078528	HCM	heart:	n/a
45	chr18:29078478-29078528	BJ	skin:	n/a
46	chr18:29078478-29078528	HRCEpiC	kidney:	n/a
47	chr18:29078478-29078528	HCPEpiC	choroid plexus:	n/a
48	chr18:29078478-29078528	MCF10A-Er-Src	breast:	n/a
49	chr18:29078478-29078528	HMEC	breast:	n/a
50	chr18:29078478-29078528	NB4	blood:	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:29078512..29082072-chr18:29089360..29094851,6	K562	blood:
2	chr18:28932546..28935472-chr18:29078101..29080400,2	K562	blood:

Variant related genes	Relation type
ENSG00000266521	TF binding region
ENSG00000266521	CpG island
ENSG00000266729	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1031729	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11081701	0.87[ASN][1000 genomes]
rs1350731	0.83[ASN][1000 genomes]
rs1460602	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17660585	0.88[ASN][1000 genomes]
rs1824477	0.81[ASN][1000 genomes]
rs1841396	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2212617	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2212618	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2219584	0.83[ASN][1000 genomes]
rs2704050	0.82[ASN][1000 genomes]
rs2704051	0.84[ASN][1000 genomes]
rs2704052	0.85[ASN][1000 genomes]
rs2704053	0.85[ASN][1000 genomes]
rs2704055	0.98[ASN][1000 genomes]
rs2848677	0.85[ASN][1000 genomes]
rs2848680	0.85[ASN][1000 genomes]
rs2848681	0.85[ASN][1000 genomes]
rs4799310	0.88[ASN][1000 genomes]
rs4799573	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6506927	0.83[ASN][1000 genomes]
rs6506928	0.83[ASN][1000 genomes]
rs7227343	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7227984	0.88[ASN][1000 genomes]
rs7231288	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7231553	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7232282	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7235272	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7236324	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7236469	0.88[ASN][1000 genomes]
rs7238729	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7240824	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7240920	0.83[EUR][1000 genomes]
rs7241107	0.81[ASN][1000 genomes]
rs73414280	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73953901	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9304097	0.83[ASN][1000 genomes]
rs9304098	0.98[ASN][1000 genomes]
rs9304099	0.88[ASN][1000 genomes]
rs9941421	0.81[ASN][1000 genomes]
rs9945031	0.88[ASN][1000 genomes]
rs9951843	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9961910	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9961920	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9961925	0.88[ASN][1000 genomes]
rs9962121	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9962318	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9962333	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9962423	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1066692	chr18:28856066-29190505	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv543674	chr18:28856066-29190505	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv916545	chr18:28898800-29166364	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv833615	chr18:29008396-29192976	Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9945420	RP11-650P15.1	cis	Heart Left Ventricle	GTEx
rs9945420	RP11-650P15.1	cis	Thyroid	GTEx
rs9945420	DSG2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:29077200-29079400	Active TSS	iPS-15b Cell Line	embryonic stem cell
2	chr18:29077200-29079600	Active TSS	Rectal Mucosa Donor 29	rectum
3	chr18:29077200-29079800	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr18:29077200-29080200	Active TSS	H1 Cell Line	embryonic stem cell
5	chr18:29077200-29080200	Active TSS	Duodenum Mucosa	Duodenum
6	chr18:29077400-29078600	Active TSS	Primary T helper naive cells fromperipheralblood	blood
7	chr18:29077400-29078800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr18:29077400-29078800	Bivalent/Poised TSS	Fetal Stomach	stomach
9	chr18:29077400-29079000	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr18:29077400-29079000	Active TSS	Liver	Liver
11	chr18:29077400-29079200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr18:29077400-29079200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
13	chr18:29077400-29079200	Active TSS	Fetal Intestine Large	intestine
14	chr18:29077400-29079200	Active TSS	Hela-S3	cervix
15	chr18:29077400-29079200	Active TSS	NH-A	brain
16	chr18:29077400-29079400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr18:29077400-29079400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr18:29077400-29079400	Active TSS	Breast Myoepithelial Primary Cells	Breast
19	chr18:29077400-29079400	Active TSS	Fetal Brain Female	brain
20	chr18:29077400-29079400	Active TSS	Left Ventricle	heart
21	chr18:29077400-29079400	Active TSS	Pancreas	Pancrea
22	chr18:29077400-29079400	Active TSS	Stomach Mucosa	stomach
23	chr18:29077400-29079600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
24	chr18:29077400-29079600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr18:29077400-29079600	Active TSS	Fetal Intestine Small	intestine
26	chr18:29077400-29079600	Active TSS	Pancreatic Islets	Pancreatic Islet
27	chr18:29077400-29079600	Active TSS	Rectal Mucosa Donor 31	rectum
28	chr18:29077400-29079600	Active TSS	Right Ventricle	heart
29	chr18:29077400-29079800	Active TSS	H9 Cell Line	embryonic stem cell
30	chr18:29077400-29080200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr18:29077400-29080200	Active TSS	HUES6 Cell Line	embryonic stem cell
32	chr18:29077400-29080400	Active TSS	Rectal Smooth Muscle	rectum
33	chr18:29077400-29080600	Active TSS	GM12878-XiMat	blood
34	chr18:29077600-29078600	Active TSS	Primary T cells from cord blood	blood
35	chr18:29077600-29078600	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr18:29077600-29078600	Active TSS	Gastric	stomach
37	chr18:29077600-29078600	Transcr. at gene 5' and 3'	Right Atrium	heart
38	chr18:29077600-29078600	Bivalent Enhancer	Spleen	Spleen
39	chr18:29077600-29079000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr18:29077600-29079000	Active TSS	Psoas Muscle	Psoas
41	chr18:29077600-29079200	Active TSS	HUES48 Cell Line	embryonic stem cell
42	chr18:29077600-29079200	Active TSS	iPS-18 Cell Line	embryonic stem cell
43	chr18:29077600-29079200	Active TSS	Ovary	ovary
44	chr18:29077600-29079200	Bivalent/Poised TSS	Small Intestine	intestine
45	chr18:29077600-29079200	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
46	chr18:29077600-29079400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr18:29077600-29079400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr18:29077600-29079400	Active TSS	A549	lung
49	chr18:29077600-29079400	Active TSS	K562	blood
50	chr18:29077600-29079600	Active TSS	Placenta Amnion	Placenta Amnion

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