Variant report

Variant	rs4662717
Chromosome Location	chr2:128013504-128013505
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:128013491..128017677-chr2:128048159..128051668,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163161	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10209678	0.96[ASN][1000 genomes]
rs10803585	0.85[ASN][1000 genomes]
rs10928761	0.89[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs11886231	0.98[ASN][1000 genomes]
rs11890187	0.90[ASN][1000 genomes]
rs12052483	0.84[ASN][1000 genomes]
rs12463451	0.93[ASN][1000 genomes]
rs12463909	0.91[EUR][1000 genomes]
rs12465955	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12469035	0.87[EUR][1000 genomes]
rs12477214	0.83[ASN][1000 genomes]
rs12479003	0.86[ASN][1000 genomes]
rs12622436	0.91[CHB][hapmap];0.98[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.90[ASN][1000 genomes]
rs12623948	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12692064	0.96[ASN][1000 genomes]
rs12989081	0.84[ASN][1000 genomes]
rs12989154	0.86[ASN][1000 genomes]
rs12991768	0.81[ASN][1000 genomes]
rs13029237	0.95[CHB][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs1566822	0.93[EUR][1000 genomes]
rs1566823	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs17015199	0.90[ASN][1000 genomes]
rs1850689	0.84[ASN][1000 genomes]
rs2090574	0.85[ASN][1000 genomes]
rs2174270	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2276583	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2896888	0.87[EUR][1000 genomes]
rs2896980	0.84[ASN][1000 genomes]
rs3088374	0.81[MEX][hapmap]
rs34832797	0.86[ASN][1000 genomes]
rs35293119	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35328149	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3768866	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs3902960	0.94[EUR][1000 genomes]
rs4150407	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4150441	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4150454	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4150477	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.98[ASN][1000 genomes]
rs4150495	0.98[ASN][1000 genomes]
rs4150496	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.98[ASN][1000 genomes]
rs4233583	1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs4233584	0.93[ASN][1000 genomes]
rs4497825	0.85[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4560059	0.91[EUR][1000 genomes]
rs4580338	0.89[EUR][1000 genomes]
rs4662575	0.99[ASN][1000 genomes]
rs4662578	0.90[ASN][1000 genomes]
rs4662580	0.82[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.89[ASN][1000 genomes]
rs4662710	0.96[CEU][hapmap];0.92[EUR][1000 genomes]
rs4662711	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4662712	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4662722	0.85[CEU][hapmap];0.89[ASN][1000 genomes]
rs4662725	0.84[ASN][1000 genomes]
rs55905117	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55998967	0.95[ASN][1000 genomes]
rs58475809	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59566504	0.87[ASN][1000 genomes]
rs62157549	0.90[ASN][1000 genomes]
rs62157555	0.89[ASN][1000 genomes]
rs6430931	0.86[EUR][1000 genomes]
rs6430935	0.98[ASN][1000 genomes]
rs6712213	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6712446	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6712551	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6731176	0.83[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.82[LWK][hapmap];0.86[MEX][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6732279	1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs6761447	0.90[ASN][1000 genomes]
rs71414745	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7568261	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7580658	0.95[CHB][hapmap];0.91[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap]
rs7585198	0.82[EUR][1000 genomes]
rs7589451	0.85[ASN][1000 genomes]
rs7591760	0.84[EUR][1000 genomes]
rs867304	0.90[ASN][1000 genomes]
rs9636235	0.93[EUR][1000 genomes]
rs9636236	0.96[CEU][hapmap];0.93[EUR][1000 genomes]
rs9636237	0.82[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.90[ASN][1000 genomes]
rs9789510	1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006112	chr2:127830117-128032546	Transcr. at gene 5' and 3' Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv1011378	chr2:127841930-128020546	Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv999809	chr2:127841930-128032546	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv1010669	chr2:127848860-128032546	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
5	nsv1003599	chr2:127871183-128059407	Strong transcription Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
6	nsv535920	chr2:127871183-128059407	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4662717	TUBA3E	cis	parietal	SCAN
rs4662717	ERCC3	cis	cerebellum	SCAN
rs4662717	ERCC3	cis	parietal	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:128002400-128015800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr2:128002800-128014000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr2:128003000-128016400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr2:128003400-128014000	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr2:128004200-128014000	Weak transcription	Fetal Lung	lung
6	chr2:128004400-128014200	Weak transcription	Primary B cells from cord blood	blood
7	chr2:128004800-128014000	Weak transcription	Fetal Thymus	thymus
8	chr2:128005000-128014400	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr2:128005000-128016400	Weak transcription	Fetal Kidney	kidney
10	chr2:128005200-128014000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr2:128005400-128016200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr2:128007600-128015800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr2:128010000-128014000	Weak transcription	Primary monocytes fromperipheralblood	blood
14	chr2:128010600-128014400	Weak transcription	Primary B cells from peripheral blood	blood
15	chr2:128010800-128014400	Weak transcription	Duodenum Mucosa	Duodenum
16	chr2:128011400-128014000	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr2:128011400-128014400	Weak transcription	NHLF	lung
18	chr2:128011600-128014000	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr2:128011600-128014000	Weak transcription	Brain Germinal Matrix	brain
20	chr2:128011800-128013800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr2:128011800-128014000	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr2:128011800-128014200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr2:128011800-128015800	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr2:128011800-128017200	Weak transcription	Small Intestine	intestine
25	chr2:128012000-128013600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr2:128012000-128013800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr2:128012000-128014400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr2:128012200-128013600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr2:128012200-128014000	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr2:128012200-128014000	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr2:128012200-128014000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr2:128012200-128014000	Weak transcription	Stomach Smooth Muscle	stomach
33	chr2:128012400-128014000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr2:128012400-128014000	Weak transcription	Primary T helper cells PMA-I stimulated	--
35	chr2:128012400-128014000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr2:128012400-128014000	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr2:128012400-128014000	Weak transcription	HUVEC	blood vessel
38	chr2:128012400-128014000	Weak transcription	Osteobl	bone
39	chr2:128012400-128014200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr2:128012400-128014200	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr2:128012400-128014400	Weak transcription	Rectal Smooth Muscle	rectum
42	chr2:128012400-128014400	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr2:128012400-128014600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr2:128012400-128014600	Weak transcription	A549	lung
45	chr2:128012400-128014600	Weak transcription	HMEC	breast
46	chr2:128012400-128015600	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr2:128012400-128016800	Weak transcription	NHDF-Ad	bronchial
48	chr2:128012400-128028000	Weak transcription	Hela-S3	cervix
49	chr2:128012600-128014200	Weak transcription	Colonic Mucosa	Colon
50	chr2:128012600-128014400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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