Variant report

Variant	rs7227984
Chromosome Location	chr18:29078627-29078628
allele	A/G
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	MXI1	chr18:29078411-29078816	K562	blood:	n/a	n/a
3	TBL1XR1	chr18:29077623-29078707	K562	blood:	n/a	n/a
4	MAX	chr18:29077454-29078702	K562	blood:	n/a	n/a
5	MAX	chr18:29077372-29078768	K562	blood:	n/a	n/a
6	SIN3A	chr18:29078123-29078628	GM12878	blood:	n/a	n/a
7	ELF1	chr18:29077711-29078655	GM12878	blood:	n/a	n/a
8	ZMIZ1	chr18:29077670-29078830	K562	blood:	n/a	n/a
9	MAX	chr18:29077944-29078631	HepG2	liver:	n/a	n/a
10	CHD2	chr18:29077693-29078755	GM12878	blood:	n/a	chr18:29077809-29077819 chr18:29078035-29078042
11	RFX5	chr18:29078478-29078678	GM12878	blood:	n/a	n/a
12	POLR2A	chr18:29077752-29078720	K562	blood:	n/a	n/a
13	SMC3	chr18:29077842-29078734	Hela-S3	cervix:	n/a	n/a
14	MAX	chr18:29077794-29078696	ECC-1	luminal epithelium:	n/a	n/a
15	E2F4	chr18:29077961-29078670	MCF10A-Er-Src	breast:	n/a	chr18:29078006-29078017 chr18:29078340-29078349 chr18:29078035-29078042
16	POLR2A	chr18:29077385-29078758	H1-hESC	embryonic stem cell:	n/a	n/a
17	POLR2A	chr18:29077369-29078739	H1-hESC	embryonic stem cell:	n/a	n/a
18	MAX	chr18:29077838-29078718	A549	lung:	n/a	n/a
19	POLR2A	chr18:29078084-29078838	GM12878	blood:	n/a	n/a
20	TAF1	chr18:29077667-29078669	ECC-1	luminal epithelium:	n/a	n/a
21	STAT3	chr18:29078584-29078652	MCF10A-Er-Src	breast:	n/a	n/a
22	POLR2A	chr18:29077620-29078715	K562	blood:	n/a	n/a
23	YY1	chr18:29077517-29078685	K562	blood:	n/a	chr18:29078340-29078349 chr18:29078403-29078417 chr18:29077999-29078011
24	POLR2A	chr18:29077487-29078653	HepG2	liver:	n/a	n/a
25	MAX	chr18:29077944-29078760	Hela-S3	cervix:	n/a	n/a
26	RAD21	chr18:29078408-29078636	H1-hESC	embryonic stem cell:	n/a	n/a
27	TFAP2C	chr18:29077718-29078777	Hela-S3	cervix:	n/a	chr18:29078083-29078098
28	GTF2F1	chr18:29078317-29078806	Hela-S3	cervix:	n/a	n/a
29	YY1	chr18:29077655-29078718	GM12878	blood:	n/a	chr18:29078340-29078349 chr18:29078403-29078417 chr18:29077999-29078011
30	JUND	chr18:29077322-29078758	K562	blood:	n/a	chr18:29077857-29077866
31	TAF7	chr18:29077349-29078695	H1-hESC	embryonic stem cell:	n/a	n/a
32	POLR2A	chr18:29077557-29078773	GM19193	blood:	n/a	n/a
33	POLR2A	chr18:29077558-29078683	GM12878	blood:	n/a	n/a
34	HEY1	chr18:29078100-29078769	K562	blood:	n/a	n/a
35	POLR2A	chr18:29077587-29078727	GM12892	blood:	n/a	n/a
36	YY1	chr18:29077694-29078635	GM12891	blood:	n/a	chr18:29078340-29078349 chr18:29078403-29078417 chr18:29077999-29078011
37	EGR1	chr18:29078455-29078648	GM12878	blood:	n/a	chr18:29078539-29078553 chr18:29078539-29078550
38	POLR2A	chr18:29077611-29079895	K562	blood:	n/a	n/a
39	UBTF	chr18:29077381-29078714	K562	blood:	n/a	n/a
40	RUNX3	chr18:29077873-29078676	GM12878	blood:	n/a	n/a
41	ZC3H11A	chr18:29078451-29078642	K562	blood:	n/a	n/a
42	POLR2A	chr18:29077612-29078702	GM18505	blood:	n/a	n/a
43	MAZ	chr18:29077643-29078743	HepG2	liver:	n/a	n/a
44	IRF1	chr18:29078525-29078867	K562	blood:	n/a	n/a
45	POLR2A	chr18:29077192-29078914	H1-hESC	embryonic stem cell:	n/a	n/a
46	MAZ	chr18:29077691-29078635	Hela-S3	cervix:	n/a	n/a
47	CUX1	chr18:29078615-29078770	K562	blood:	n/a	n/a
48	MAX	chr18:29077384-29078698	HepG2	liver:	n/a	n/a
49	TAF1	chr18:29077594-29078747	K562	blood:	n/a	n/a
50	EGR1	chr18:29078386-29078713	K562	blood:	n/a	chr18:29078539-29078553 chr18:29078539-29078550

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
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	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs1350731	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1460602	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs17660585	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1824477	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1841396	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs2212617	0.89[ASN][1000 genomes]
rs2212618	1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs2219584	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2704050	0.93[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2704051	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2704052	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2704053	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2704055	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2848677	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2848680	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2848681	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4799310	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4799573	1.00[ASN][1000 genomes]
rs6506927	0.94[CHB][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6506928	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7227343	0.90[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs7231288	0.98[ASN][1000 genomes]
rs7231553	0.98[ASN][1000 genomes]
rs7232282	1.00[ASN][1000 genomes]
rs7235272	0.98[ASN][1000 genomes]
rs7236324	1.00[ASN][1000 genomes]
rs7236469	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7238729	0.98[ASN][1000 genomes]
rs7239805	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7240824	0.83[ASN][1000 genomes]
rs7240920	0.90[ASN][1000 genomes]
rs7241107	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73414280	0.99[ASN][1000 genomes]
rs73953901	1.00[ASN][1000 genomes]
rs9304097	0.91[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9304098	0.96[CEU][hapmap];0.90[CHB][hapmap];0.83[CHD][hapmap];0.81[JPT][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9304099	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9941421	0.89[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9945031	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9945420	0.88[ASN][1000 genomes]
rs9951843	0.94[ASN][1000 genomes]
rs9961910	0.96[ASN][1000 genomes]
rs9961920	1.00[ASN][1000 genomes]
rs9961925	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9962121	0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];1.00[ASN][1000 genomes]
rs9962318	1.00[ASN][1000 genomes]
rs9962333	0.88[ASN][1000 genomes]
rs9962423	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[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
rs7227984	DSC1	cis	parietal	SCAN
rs7227984	DSG2	Cis_1M	lymphoblastoid	RTeQTL
rs7227984	RP11-650P15.1	cis	Thyroid	GTEx

Chromatin state (count:111 , 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	chr18:29077400-29078800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr18:29077400-29078800	Bivalent/Poised TSS	Fetal Stomach	stomach
8	chr18:29077400-29079000	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr18:29077400-29079000	Active TSS	Liver	Liver
10	chr18:29077400-29079200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr18:29077400-29079200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
12	chr18:29077400-29079200	Active TSS	Fetal Intestine Large	intestine
13	chr18:29077400-29079200	Active TSS	Hela-S3	cervix
14	chr18:29077400-29079200	Active TSS	NH-A	brain
15	chr18:29077400-29079400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr18:29077400-29079400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr18:29077400-29079400	Active TSS	Breast Myoepithelial Primary Cells	Breast
18	chr18:29077400-29079400	Active TSS	Fetal Brain Female	brain
19	chr18:29077400-29079400	Active TSS	Left Ventricle	heart
20	chr18:29077400-29079400	Active TSS	Pancreas	Pancrea
21	chr18:29077400-29079400	Active TSS	Stomach Mucosa	stomach
22	chr18:29077400-29079600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
23	chr18:29077400-29079600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr18:29077400-29079600	Active TSS	Fetal Intestine Small	intestine
25	chr18:29077400-29079600	Active TSS	Pancreatic Islets	Pancreatic Islet
26	chr18:29077400-29079600	Active TSS	Rectal Mucosa Donor 31	rectum
27	chr18:29077400-29079600	Active TSS	Right Ventricle	heart
28	chr18:29077400-29079800	Active TSS	H9 Cell Line	embryonic stem cell
29	chr18:29077400-29080200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr18:29077400-29080200	Active TSS	HUES6 Cell Line	embryonic stem cell
31	chr18:29077400-29080400	Active TSS	Rectal Smooth Muscle	rectum
32	chr18:29077400-29080600	Active TSS	GM12878-XiMat	blood
33	chr18:29077600-29079000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr18:29077600-29079000	Active TSS	Psoas Muscle	Psoas
35	chr18:29077600-29079200	Active TSS	HUES48 Cell Line	embryonic stem cell
36	chr18:29077600-29079200	Active TSS	iPS-18 Cell Line	embryonic stem cell
37	chr18:29077600-29079200	Active TSS	Ovary	ovary
38	chr18:29077600-29079200	Bivalent/Poised TSS	Small Intestine	intestine
39	chr18:29077600-29079200	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
40	chr18:29077600-29079400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr18:29077600-29079400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr18:29077600-29079400	Active TSS	A549	lung
43	chr18:29077600-29079400	Active TSS	K562	blood
44	chr18:29077600-29079600	Active TSS	Placenta Amnion	Placenta Amnion
45	chr18:29077600-29080200	Active TSS	iPS-20b Cell Line	embryonic stem cell
46	chr18:29077600-29080200	Active TSS	Colonic Mucosa	Colon
47	chr18:29077800-29078800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr18:29077800-29078800	Bivalent/Poised TSS	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr18:29077800-29078800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr18:29077800-29078800	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain

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