Variant report

Variant	rs807936
Chromosome Location	chr3:47322496-47322497
allele	C/T
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	POLR2A	chr3:47321384-47325284	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr3:47321796-47324876	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr3:47322035-47322716	K562	blood:	n/a	n/a
4	POLR2A	chr3:47322106-47322765	HepG2	liver:	n/a	n/a
5	POLR2A	chr3:47322145-47323720	A549	lung:	n/a	n/a
6	POLR2A	chr3:47322096-47324639	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr3:47322067-47324681	IMR90	lung:	n/a	n/a
8	SPI1	chr3:47322293-47322598	GM12878	blood:	n/a	chr3:47322488-47322497
9	POLR2A	chr3:47321218-47324899	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:47321814..47325452-chr3:47418885..47424380,8	K562	blood:
2	chr3:47318429..47320664-chr3:47321864..47324822,2	MCF-7	breast:
3	chr3:47204122..47207133-chr3:47321636..47325818,4	K562	blood:

Variant related genes	Relation type
KIF9	TF binding region
KLHL18	TF binding region
ENSG00000227398	Chromatin interaction
ENSG00000181555	Chromatin interaction
ENSG00000076201	Chromatin interaction
ENSG00000260236	Chromatin interaction
ENSG00000088727	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs1038394	0.85[ASW][hapmap];0.96[CEU][hapmap];0.81[JPT][hapmap];0.95[LWK][hapmap];0.88[MEX][hapmap];0.96[MKK][hapmap];0.93[TSI][hapmap];0.89[YRI][hapmap]
rs1076394	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.98[TSI][hapmap];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10865946	0.96[CEU][hapmap];0.89[YRI][hapmap]
rs11130115	0.93[ASW][hapmap];0.89[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.81[LWK][hapmap];0.92[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap]
rs11130123	0.93[ASW][hapmap];0.96[CEU][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.92[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11130124	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11130126	0.92[CEU][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes]
rs11130128	0.96[CEU][hapmap];0.81[JPT][hapmap]
rs11130129	0.96[CEU][hapmap];0.82[JPT][hapmap]
rs11705957	0.96[CEU][hapmap];0.80[GIH][hapmap];0.81[JPT][hapmap];0.93[TSI][hapmap]
rs11710013	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.92[MEX][hapmap];0.83[MKK][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11710121	0.85[CEU][hapmap]
rs11710322	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.98[TSI][hapmap];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11711824	0.85[ASW][hapmap];0.96[CEU][hapmap];0.81[JPT][hapmap];0.90[LWK][hapmap];0.83[MEX][hapmap];0.96[MKK][hapmap];0.93[TSI][hapmap];0.84[YRI][hapmap]
rs11712445	0.96[CEU][hapmap];0.89[YRI][hapmap]
rs11714294	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11716763	0.96[CEU][hapmap];0.82[GIH][hapmap];0.81[JPT][hapmap];0.84[TSI][hapmap]
rs11719877	0.85[ASW][hapmap];0.96[CEU][hapmap];0.80[GIH][hapmap];0.95[LWK][hapmap];0.88[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap]
rs11915074	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs11920853	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs11921117	0.85[EUR][1000 genomes]
rs12636851	0.96[CEU][hapmap];0.81[JPT][hapmap];0.91[TSI][hapmap]
rs13061071	0.93[ASW][hapmap];0.89[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.81[LWK][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap]
rs13072802	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13075233	0.85[ASW][hapmap];0.96[CEU][hapmap];0.80[GIH][hapmap];0.95[LWK][hapmap];0.88[MEX][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap]
rs13094438	0.93[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.92[MEX][hapmap];0.89[MKK][hapmap];0.98[TSI][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1531875	0.85[ASW][hapmap];0.96[CEU][hapmap];0.81[JPT][hapmap];0.95[LWK][hapmap];0.88[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap]
rs1638676	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17080872	0.81[JPT][hapmap]
rs17410853	0.85[CEU][hapmap]
rs17411375	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.98[TSI][hapmap]
rs17476234	0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1872164	0.96[CEU][hapmap];0.80[GIH][hapmap];0.81[JPT][hapmap];0.93[TSI][hapmap]
rs2101247	0.92[CEU][hapmap];0.81[JPT][hapmap];0.88[TSI][hapmap]
rs2132173	0.93[ASW][hapmap];0.89[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.81[LWK][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap]
rs2159400	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap]
rs2276853	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.98[TSI][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2276854	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.98[TSI][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs295428	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.96[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes]
rs295433	0.95[YRI][hapmap]
rs295441	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs295442	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs295449	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap]
rs295458	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap]
rs295461	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.81[AFR][1000 genomes]
rs3736177	0.96[CEU][hapmap]
rs4078466	0.85[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap]
rs4082155	0.93[ASW][hapmap];0.85[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.81[LWK][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap]
rs4682852	0.89[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap]
rs4683326	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4858811	0.96[CEU][hapmap];0.81[JPT][hapmap]
rs4858824	0.96[CEU][hapmap]
rs4858868	0.85[ASW][hapmap];0.96[CEU][hapmap];0.93[LWK][hapmap];0.88[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap]
rs4858893	0.96[CEU][hapmap];0.85[JPT][hapmap]
rs4858894	0.87[CEU][hapmap];0.88[JPT][hapmap];0.89[YRI][hapmap]
rs59689369	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6767907	0.81[CEU][hapmap];0.89[TSI][hapmap]
rs6768221	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs6772670	0.95[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap]
rs6780013	0.89[CEU][hapmap];0.86[TSI][hapmap]
rs6791842	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6792461	0.96[CEU][hapmap];0.81[JPT][hapmap];0.91[TSI][hapmap]
rs6800271	0.96[CEU][hapmap];0.81[JPT][hapmap];0.93[TSI][hapmap]
rs7636423	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7651762	0.96[CEU][hapmap];0.81[JPT][hapmap]
rs807932	0.92[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs807935	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs807937	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs811115	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs878659	0.85[ASW][hapmap];0.96[CEU][hapmap];0.81[JPT][hapmap];0.95[LWK][hapmap];0.88[MEX][hapmap];0.96[MKK][hapmap];0.91[TSI][hapmap];0.89[YRI][hapmap]
rs922957	0.96[CEU][hapmap]
rs9311403	0.84[CEU][hapmap]
rs9683033	0.85[ASW][hapmap];0.96[CEU][hapmap];0.81[JPT][hapmap];0.95[LWK][hapmap];0.88[MEX][hapmap];0.96[MKK][hapmap];0.91[TSI][hapmap];0.89[YRI][hapmap]
rs9837343	0.81[CEU][hapmap];0.89[TSI][hapmap]

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	nsv876756	chr3:47002931-47586514	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
2	nsv1007714	chr3:47084387-47331570	Transcr. at gene 5' and 3' Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	nsv1014457	chr3:47222292-47335175	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
4	nsv536560	chr3:47222292-47335175	Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs807936	KLHL18	Cis_1M	lymphoblastoid	RTeQTL
rs807936	SCAP	cis	parietal	SCAN
rs807936	SETD2	Cis_1M	lymphoblastoid	RTeQTL
rs807936	RTP3	cis	lesional skin	skin_eQTL
rs807936	HYAL2	cis	cerebellum	SCAN
rs807936	CCDC12	cis	cerebellum	SCAN
rs807936	C3orf75	cis	cerebellum	SCAN
rs807936	NCKIPSD	cis	cerebellum	SCAN
rs807936	PRKAR2A	cis	cerebellum	SCAN
rs807936	AMIGO3	cis	cerebellum	SCAN

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47293600-47323200	Weak transcription	Spleen	Spleen
2	chr3:47300800-47322800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr3:47301000-47322800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr3:47301200-47323000	Weak transcription	Psoas Muscle	Psoas
5	chr3:47302800-47323200	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr3:47305600-47323200	Weak transcription	Primary T cells from cord blood	blood
7	chr3:47308600-47323000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr3:47308600-47323200	Weak transcription	Esophagus	oesophagus
9	chr3:47308800-47322600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr3:47308800-47322600	Weak transcription	Brain Anterior Caudate	brain
11	chr3:47308800-47322600	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr3:47308800-47322800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr3:47308800-47322800	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr3:47308800-47323000	Weak transcription	Adipose Nuclei	Adipose
15	chr3:47308800-47323000	Weak transcription	Brain Substantia Nigra	brain
16	chr3:47309000-47322600	Weak transcription	HUVEC	blood vessel
17	chr3:47309000-47322800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr3:47309000-47322800	Weak transcription	Brain Hippocampus Middle	brain
19	chr3:47309000-47323000	Weak transcription	Colon Smooth Muscle	Colon
20	chr3:47309000-47323200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr3:47309000-47323200	Weak transcription	Brain Cingulate Gyrus	brain
22	chr3:47309200-47322600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr3:47309200-47323200	Weak transcription	HSMMtube	muscle
24	chr3:47311000-47322800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr3:47312400-47323000	Weak transcription	Primary neutrophils fromperipheralblood	blood
26	chr3:47312600-47322600	Weak transcription	Primary monocytes fromperipheralblood	blood
27	chr3:47312600-47322800	Weak transcription	Monocytes-CD14+_RO01746	blood
28	chr3:47314800-47323200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr3:47315600-47322600	Weak transcription	Fetal Intestine Large	intestine
30	chr3:47316200-47323000	Weak transcription	Fetal Stomach	stomach
31	chr3:47316200-47323200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr3:47317800-47323000	Weak transcription	Fetal Muscle Leg	muscle
33	chr3:47318600-47322600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr3:47318600-47322600	Weak transcription	Left Ventricle	heart
35	chr3:47319200-47322600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr3:47319200-47322600	Weak transcription	Fetal Thymus	thymus
37	chr3:47321400-47323200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr3:47321800-47323000	Enhancers	Pancreas	Pancrea
39	chr3:47322000-47322600	Enhancers	Breast Myoepithelial Primary Cells	Breast
40	chr3:47322200-47322600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr3:47322200-47322600	Weak transcription	Liver	Liver
42	chr3:47322200-47322600	Enhancers	Fetal Brain Female	brain
43	chr3:47322200-47322600	Enhancers	Rectal Mucosa Donor 31	rectum
44	chr3:47322200-47322600	Enhancers	Hela-S3	cervix
45	chr3:47322200-47322600	Enhancers	K562	blood
46	chr3:47322200-47322800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr3:47322200-47322800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr3:47322200-47323000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr3:47322200-47323000	Enhancers	Gastric	stomach
50	chr3:47322200-47323000	Enhancers	Stomach Smooth Muscle	stomach

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