Variant report

Variant	rs17074680
Chromosome Location	chr3:42671668-42671669
allele	G/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	chr3:42671338-42671683	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:42630327..42632728-chr3:42670152..42672818,2	MCF-7	breast:

Variant related genes	Relation type
NKTR	TF binding region
ENSG00000008324	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs1062051	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs13072295	0.89[ASN][1000 genomes]
rs13085695	0.81[ASN][1000 genomes]
rs13089845	0.89[ASN][1000 genomes]
rs13090902	0.89[ASN][1000 genomes]
rs13093680	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs13095447	0.86[ASN][1000 genomes]
rs17074602	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs17074662	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs17074664	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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17074669	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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17074673	0.89[ASN][1000 genomes]
rs17074674	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs17074693	0.97[ASN][1000 genomes]
rs2241542	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs2284303	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2284304	0.89[ASN][1000 genomes]
rs2300057	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs2300058	0.89[ASN][1000 genomes]
rs2302352	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs33969824	0.97[ASN][1000 genomes]
rs339713	1.00[CEU][hapmap];0.86[GIH][hapmap];0.81[EUR][1000 genomes]
rs33984028	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs34683820	0.89[ASN][1000 genomes]
rs34687113	0.97[ASN][1000 genomes]
rs34762478	0.94[ASN][1000 genomes]
rs34801786	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[ASN][1000 genomes]
rs34852409	0.90[ASN][1000 genomes]
rs34977988	0.82[ASN][1000 genomes]
rs35506005	0.92[ASN][1000 genomes]
rs35676838	0.89[ASN][1000 genomes]
rs35770315	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35890296	0.89[ASN][1000 genomes]
rs36033201	0.89[ASN][1000 genomes]
rs3774401	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs3774402	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs3774404	0.97[ASN][1000 genomes]
rs3774406	0.92[ASN][1000 genomes]
rs3774407	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs3821836	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3846058	0.97[ASN][1000 genomes]
rs3846059	1.00[CHB][hapmap];0.95[CHD][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs3846061	1.00[CEU][hapmap]
rs3856737	0.89[ASN][1000 genomes]
rs3886782	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3901239	1.00[CEU][hapmap];0.86[GIH][hapmap];0.81[EUR][1000 genomes]
rs4371488	1.00[YRI][hapmap]
rs56797870	0.89[ASN][1000 genomes]
rs57259216	0.89[ASN][1000 genomes]
rs58868911	0.89[ASN][1000 genomes]
rs59914338	0.97[ASN][1000 genomes]
rs60348477	0.94[ASN][1000 genomes]
rs61149998	0.97[ASN][1000 genomes]
rs6441928	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs66786953	0.90[ASN][1000 genomes]
rs67165547	0.89[ASN][1000 genomes]
rs67533173	0.93[ASN][1000 genomes]
rs6772312	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6778982	0.89[ASN][1000 genomes]
rs6788548	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs6793186	0.89[ASN][1000 genomes]
rs6795296	0.89[ASN][1000 genomes]
rs68028490	0.92[ASN][1000 genomes]
rs68071013	0.97[ASN][1000 genomes]
rs72864072	0.89[ASN][1000 genomes]
rs7617403	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7617736	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7624628	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs9647353	1.00[YRI][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002944	chr3:42559762-42728909	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42643200-42672800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:42643600-42675000	Weak transcription	Aorta	Aorta
3	chr3:42644000-42672000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr3:42644200-42672400	Weak transcription	Fetal Kidney	kidney
5	chr3:42646000-42672000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr3:42647200-42688200	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr3:42647400-42672000	Weak transcription	NHLF	lung
8	chr3:42647600-42672000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr3:42647600-42677600	Weak transcription	Gastric	stomach
10	chr3:42648800-42672600	Weak transcription	Fetal Brain Female	brain
11	chr3:42650400-42671800	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr3:42650400-42672000	Weak transcription	Stomach Smooth Muscle	stomach
13	chr3:42650600-42672600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr3:42650600-42673000	Weak transcription	Esophagus	oesophagus
15	chr3:42650800-42672800	Weak transcription	Ovary	ovary
16	chr3:42651200-42693000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr3:42651800-42680400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr3:42653400-42672000	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr3:42653600-42672600	Weak transcription	Lung	lung
20	chr3:42653600-42672600	Weak transcription	Pancreas	Pancrea
21	chr3:42655000-42672400	Weak transcription	Right Ventricle	heart
22	chr3:42655000-42677800	Weak transcription	Small Intestine	intestine
23	chr3:42655200-42672000	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr3:42655400-42672000	Weak transcription	Brain Cingulate Gyrus	brain
25	chr3:42655400-42674400	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr3:42656200-42688400	Strong transcription	Monocytes-CD14+_RO01746	blood
27	chr3:42656600-42673000	Strong transcription	Hela-S3	cervix
28	chr3:42657400-42679600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr3:42657800-42672000	Weak transcription	Brain Angular Gyrus	brain
30	chr3:42658200-42673000	Weak transcription	Rectal Smooth Muscle	rectum
31	chr3:42658200-42682200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr3:42658200-42693000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
33	chr3:42658400-42691400	Strong transcription	Dnd41	blood
34	chr3:42658600-42677600	Weak transcription	Psoas Muscle	Psoas
35	chr3:42658600-42678400	Strong transcription	Primary T helper cells fromperipheralblood	blood
36	chr3:42659000-42673000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr3:42659000-42688000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr3:42660000-42672200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr3:42660000-42673000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr3:42660000-42679000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr3:42660800-42672600	Weak transcription	Colonic Mucosa	Colon
42	chr3:42661600-42674400	Weak transcription	Fetal Heart	heart
43	chr3:42661800-42672000	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr3:42662000-42672800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr3:42663400-42671800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr3:42663400-42672800	Weak transcription	Spleen	Spleen
47	chr3:42663600-42672000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
48	chr3:42663600-42672600	Weak transcription	Colon Smooth Muscle	Colon
49	chr3:42663800-42672000	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr3:42664200-42671800	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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