Variant report

Variant	rs9844736
Chromosome Location	chr3:52931971-52931972
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:26)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:26 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr3:52930503-52932335	IMR90	lung:	n/a	n/a
2	POLR2A	chr3:52931354-52931993	MCF10A-Er-Src	breast:	n/a	n/a
3	ZNF263	chr3:52931929-52932344	HEK293-T-REx	kidney:	n/a	n/a
4	FOS	chr3:52931922-52931975	MCF10A-Er-Src	breast:	n/a	n/a
5	POLR2A	chr3:52931433-52932079	H1-hESC	embryonic stem cell:	n/a	n/a
6	MAZ	chr3:52930977-52932117	IMR90	lung:	n/a	chr3:52931778-52931789
7	IKZF1	chr3:52931866-52931999	GM12878	blood:	n/a	n/a
8	REST	chr3:52931124-52932264	H1-neurons	neurons:	n/a	chr3:52931847-52931860
9	MYC	chr3:52931460-52932100	MCF10A-Er-Src	breast:	n/a	chr3:52931778-52931789
10	RUNX3	chr3:52931348-52932001	GM12878	blood:	n/a	chr3:52931793-52931808 chr3:52931531-52931548
11	ZEB1	chr3:52931428-52932048	GM12878	blood:	n/a	chr3:52931781-52931788
12	GATA1	chr3:52931166-52932073	PBDE	blood:	n/a	n/a
13	POLR2A	chr3:52931236-52932009	ECC-1	luminal epithelium:	n/a	n/a
14	MXI1	chr3:52931596-52931973	H1-hESC	embryonic stem cell:	n/a	n/a
15	ZEB1	chr3:52931419-52932018	HepG2	liver:	n/a	chr3:52931781-52931788
16	TAF1	chr3:52931334-52931989	H1-hESC	embryonic stem cell:	n/a	n/a
17	MAX	chr3:52931104-52931986	ECC-1	luminal epithelium:	n/a	chr3:52931778-52931789
18	RFX5	chr3:52931278-52931999	Hela-S3	cervix:	n/a	n/a
19	MAX	chr3:52931278-52932001	H1-hESC	embryonic stem cell:	n/a	chr3:52931778-52931789
20	MXI1	chr3:52930472-52932499	SK-N-SH	brain:	n/a	n/a
21	RCOR1	chr3:52931370-52932024	Hela-S3	cervix:	n/a	n/a
22	HCFC1	chr3:52931059-52932058	Hela-S3	cervix:	n/a	n/a
23	POLR2A	chr3:52931366-52931978	MCF10A-Er-Src	breast:	n/a	n/a
24	MYC	chr3:52930998-52932001	H1-hESC	embryonic stem cell:	n/a	chr3:52931778-52931789
25	RFX5	chr3:52930810-52932346	SK-N-SH	brain:	n/a	n/a
26	TAF1	chr3:52931104-52931997	ECC-1	luminal epithelium:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:52931946-52931996	HCF	heart:	n/a
2	chr3:52931946-52931996	HUVEC	blood vessel:	n/a
3	chr3:52931946-52931996	NHBE	bronchial:	n/a
4	chr3:52931946-52931996	HAEpiC	amniotic membrane:	n/a
5	chr3:52931946-52931996	ovcar-3	ovarian:	n/a
6	chr3:52931946-52931996	CMK	blood:	n/a
7	chr3:52931946-52931996	T-47D	breast:	n/a
8	chr3:52931946-52931996	MCF10A-Er-Src	breast:	n/a
9	chr3:52931946-52931996	GM19239	blood:	n/a
10	chr3:52931946-52931996	Jurkat	blood:	n/a
11	chr3:52931946-52931996	K562	blood:	n/a
12	chr3:52931946-52931996	PANC-1	pancreas:	n/a
13	chr3:52931946-52931996	HRE	kidney:	n/a
14	chr3:52931946-52931996	AoSMC	blood vessel:	n/a
15	chr3:52931946-52931996	NHDF-neo	bronchial:	n/a
16	chr3:52931946-52931996	AG09319	gingival:	n/a
17	chr3:52931946-52931996	HEK293	kidney:	embryo
18	chr3:52931946-52931996	HCPEpiC	choroid plexus:	n/a
19	chr3:52931946-52931996	HL-60	blood:	n/a
20	chr3:52931946-52931996	NH-A	brain:	n/a
21	chr3:52931946-52931996	GM06990	blood:	n/a
22	chr3:52931946-52931996	AG04449	skin:	fetal
23	chr3:52931946-52931996	PFSK-1	brain:	n/a
24	chr3:52931946-52931996	H1-hESC	embryonic stem cell:	embryo
25	chr3:52931946-52931996	GM12878	blood:	n/a
26	chr3:52931946-52931996	GM12891	blood:	n/a
27	chr3:52931946-52931996	ECC-1	luminal epithelium:	n/a
28	chr3:52931946-52931996	LNCaP	prostate:	n/a
29	chr3:52931946-52931996	HMEC	breast:	n/a
30	chr3:52931946-52931996	AG04450	lung:	fetal
31	chr3:52931946-52931996	GM12892	blood:	n/a
32	chr3:52931946-52931996	HCM	heart:	n/a
33	chr3:52931946-52931996	HRCEpiC	kidney:	n/a
34	chr3:52931946-52931996	Hela-S3	cervix:	n/a
35	chr3:52931946-52931996	HEEpiC	esophagus:	n/a
36	chr3:52931946-52931996	PrEC	prostate:	n/a
37	chr3:52931946-52931996	IMR90	lung:	fetal
38	chr3:52931946-52931996	RPTEC	kidney:	n/a
39	chr3:52931946-52931996	SK-N-MC	brain:	n/a
40	chr3:52931946-52931996	HepG2	liver:	n/a
41	chr3:52931946-52931996	HPAEpiC	pulmonary alveolar:	n/a
42	chr3:52931946-52931996	BJ	skin:	n/a
43	chr3:52931946-52931996	Caco-2	colon:	n/a
44	chr3:52931946-52931996	ProgFib	skin:	n/a
45	chr3:52931946-52931996	AG10803	skin:	n/a
46	chr3:52931946-52931996	MCF-7	breast:	n/a
47	chr3:52931946-52931996	NT2-D1	testis:	n/a
48	chr3:52931946-52931996	U87	brain:	n/a
49	chr3:52931946-52931996	HIPEpiC	eye:	n/a
50	chr3:52931946-52931996	SKMC	muscle:	n/a

No data

Variant related genes	Relation type
TMEM110-MUSTN1	TF binding region
TMEM110	TF binding region
TMEM110	CpG island
TMEM110-MUSTN1	CpG island

Extended variants
information (count: 87 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs11130331	0.95[JPT][hapmap]
rs11130332	0.84[EUR][1000 genomes]
rs1134546	1.00[CEU][hapmap];0.96[GIH][hapmap];0.97[TSI][hapmap];0.97[EUR][1000 genomes]
rs11707576	0.83[EUR][1000 genomes]
rs11708223	0.84[EUR][1000 genomes]
rs11922975	0.95[JPT][hapmap]
rs12492391	0.81[JPT][hapmap]
rs13072536	0.80[CEU][hapmap];0.81[JPT][hapmap]
rs13082061	0.85[EUR][1000 genomes]
rs13083728	0.82[CEU][hapmap];0.86[JPT][hapmap];0.80[TSI][hapmap]
rs1573815	0.82[CEU][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.80[TSI][hapmap]
rs17304995	1.00[CEU][hapmap];0.82[CHB][hapmap];0.88[TSI][hapmap]
rs2239547	0.86[JPT][hapmap]
rs2246556	0.84[CEU][hapmap];0.81[GIH][hapmap]
rs2255107	0.82[CEU][hapmap]
rs2276815	0.86[JPT][hapmap]
rs2276817	0.82[CEU][hapmap];0.86[JPT][hapmap];0.80[TSI][hapmap]
rs2276825	0.94[CEU][hapmap];0.86[JPT][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes]
rs2336162	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2336666	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2336668	0.81[JPT][hapmap]
rs2336669	1.00[CEU][hapmap];0.92[GIH][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes]
rs2336671	0.80[EUR][1000 genomes]
rs2564947	1.00[CEU][hapmap];0.95[TSI][hapmap]
rs2581780	1.00[CEU][hapmap]
rs2581797	0.84[EUR][1000 genomes]
rs2581801	0.93[ASW][hapmap];1.00[CEU][hapmap];0.92[GIH][hapmap];0.82[LWK][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2581802	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2581805	0.84[EUR][1000 genomes]
rs2581810	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs2581815	1.00[CEU][hapmap];0.95[TSI][hapmap];0.84[EUR][1000 genomes]
rs2581820	0.82[EUR][1000 genomes]
rs2581823	0.81[EUR][1000 genomes]
rs2710342	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2710345	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2878762	0.87[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs35380116	0.82[EUR][1000 genomes]
rs3733047	0.82[CEU][hapmap];0.86[JPT][hapmap];0.80[TSI][hapmap]
rs4302374	0.94[CEU][hapmap];0.81[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4519686	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[GIH][hapmap];0.85[LWK][hapmap];0.95[TSI][hapmap];0.81[YRI][hapmap];0.83[EUR][1000 genomes]
rs4687554	0.82[CEU][hapmap];0.86[JPT][hapmap];0.80[TSI][hapmap]
rs4687559	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4687560	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4687657	0.86[JPT][hapmap]
rs4687658	0.82[CEU][hapmap];0.86[JPT][hapmap]
rs4687663	0.82[CEU][hapmap];0.81[JPT][hapmap]
rs4687672	0.81[CEU][hapmap];0.86[JPT][hapmap]
rs4687680	0.81[JPT][hapmap]
rs4687682	0.81[JPT][hapmap]
rs4687687	0.90[JPT][hapmap]
rs6445538	0.82[CEU][hapmap];0.86[JPT][hapmap];0.85[TSI][hapmap]
rs6445539	0.82[CEU][hapmap];0.86[JPT][hapmap];0.85[TSI][hapmap]
rs6445547	0.93[CEU][hapmap];0.81[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6445550	1.00[CEU][hapmap];0.88[GIH][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs6768844	0.93[ASW][hapmap];1.00[CEU][hapmap];0.92[GIH][hapmap];0.88[LWK][hapmap];0.95[TSI][hapmap];0.86[YRI][hapmap];0.83[EUR][1000 genomes]
rs6770957	0.83[EUR][1000 genomes]
rs6771610	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs6773040	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6792578	0.93[ASW][hapmap];1.00[CEU][hapmap];0.92[GIH][hapmap];0.91[LWK][hapmap];0.95[TSI][hapmap];0.86[YRI][hapmap];0.83[EUR][1000 genomes]
rs6795646	0.81[JPT][hapmap]
rs6797399	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6803519	0.82[CEU][hapmap];0.86[JPT][hapmap];0.85[TSI][hapmap]
rs7621939	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7626551	0.95[JPT][hapmap]
rs7648514	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs7652131	0.83[EUR][1000 genomes]
rs9311485	1.00[CEU][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes]
rs9682464	0.94[CEU][hapmap];0.86[JPT][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9810807	0.81[JPT][hapmap]
rs9812543	0.83[EUR][1000 genomes]
rs9831409	0.84[EUR][1000 genomes]
rs9836178	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9836499	0.80[JPT][hapmap]
rs9839035	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9842974	0.83[EUR][1000 genomes]
rs9846976	1.00[CEU][hapmap];0.88[GIH][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes]
rs9847024	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9850563	0.81[JPT][hapmap]
rs9860296	0.81[JPT][hapmap]
rs9865094	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs9870898	1.00[CEU][hapmap];0.88[TSI][hapmap]
rs9876403	0.94[CEU][hapmap];0.92[GIH][hapmap];0.81[JPT][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9880978	0.81[JPT][hapmap]
rs9985365	0.95[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2762328	chr3:52774884-53002150	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	esv3446915	chr3:52786850-53049217	Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	esv3339338	chr3:52930462-52933260	Active TSS Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:16)

SNP	Gene	Cis/trans	Tissue	Source
rs9844736	TMEM110	cis	cerebellum	SCAN
rs9844736	ITIH4-AS1	cis	Artery Aorta	GTEx
rs9844736	ITIH4	cis	parietal	SCAN
rs9844736	TMEM110	cis	parietal	SCAN
rs9844736	CHDH	cis	parietal	SCAN
rs9844736	ITIH4	cis	lymphoblastoid	seeQTL
rs9844736	NEK4	cis	parietal	SCAN
rs9844736	SEMA3G	cis	parietal	SCAN
rs9844736	GNL3	cis	cerebellum	SCAN
rs9844736	AMT	cis	parietal	SCAN
rs9844736	GNL3	cis	parietal	SCAN
rs9844736	ITIH4	cis	cerebellum	SCAN
rs9844736	ITIH4-AS1	cis	lung	GTEx
rs9844736	MUSTN1	cis	Artery Aorta	GTEx
rs9844736	ITIH4-AS1	cis	Artery Tibial	GTEx
rs9844736	NT5DC2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52929800-52932200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr3:52929800-52932200	Flanking Active TSS	Primary hematopoietic stem cells	blood
3	chr3:52930000-52932000	Active TSS	H9 Cell Line	embryonic stem cell
4	chr3:52930000-52932200	Active TSS	HUES64 Cell Line	embryonic stem cell
5	chr3:52930000-52932200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr3:52930200-52932000	Active TSS	HUES6 Cell Line	embryonic stem cell
7	chr3:52930200-52932000	Active TSS	Right Atrium	heart
8	chr3:52930200-52932200	Active TSS	HUES48 Cell Line	embryonic stem cell
9	chr3:52930200-52932200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr3:52930200-52932200	Active TSS	GM12878-XiMat	blood
11	chr3:52930400-52932000	Active TSS	ES-I3 Cell Line	embryonic stem cell
12	chr3:52930400-52932000	Active TSS	iPS-15b Cell Line	embryonic stem cell
13	chr3:52930400-52932000	Active TSS	iPS-20b Cell Line	embryonic stem cell
14	chr3:52930400-52932000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr3:52930400-52932000	Active TSS	Aorta	Aorta
16	chr3:52930400-52932200	Active TSS	H1 Cell Line	embryonic stem cell
17	chr3:52930400-52932200	Active TSS	Fetal Kidney	kidney
18	chr3:52930400-52932200	Active TSS	Pancreatic Islets	Pancreatic Islet
19	chr3:52930400-52932200	Active TSS	Ovary	ovary
20	chr3:52930600-52932000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
21	chr3:52930600-52932000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr3:52930600-52932000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr3:52930600-52932000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr3:52930600-52932000	Flanking Active TSS	Primary B cells from cord blood	blood
25	chr3:52930800-52932000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr3:52930800-52932000	Active TSS	iPS-18 Cell Line	embryonic stem cell
27	chr3:52930800-52932000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr3:52930800-52932000	Active TSS	Esophagus	oesophagus
29	chr3:52930800-52932000	Active TSS	A549	lung
30	chr3:52930800-52932200	Active TSS	NHLF	lung
31	chr3:52931000-52932000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr3:52931000-52932000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr3:52931000-52932000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr3:52931000-52932000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
35	chr3:52931000-52932000	Active TSS	Brain Angular Gyrus	brain
36	chr3:52931000-52932000	Active TSS	Brain Cingulate Gyrus	brain
37	chr3:52931000-52932000	Active TSS	Brain Hippocampus Middle	brain
38	chr3:52931000-52932000	Active TSS	Colon Smooth Muscle	Colon
39	chr3:52931000-52932000	Active TSS	Fetal Intestine Large	intestine
40	chr3:52931000-52932000	Active TSS	Left Ventricle	heart
41	chr3:52931000-52932000	Active TSS	Lung	lung
42	chr3:52931000-52932000	Active TSS	Placenta Amnion	Placenta Amnion
43	chr3:52931000-52932000	Active TSS	Psoas Muscle	Psoas
44	chr3:52931000-52932000	Active TSS	Sigmoid Colon	Sigmoid Colon
45	chr3:52931000-52932000	Active TSS	Small Intestine	intestine
46	chr3:52931000-52932200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr3:52931000-52932200	Active TSS	Right Ventricle	heart
48	chr3:52931000-52932200	Active TSS	HSMM	muscle
49	chr3:52931000-52932200	Active TSS	NH-A	brain
50	chr3:52931200-52932000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived

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