Variant report

Variant	rs2236951
Chromosome Location	chr3:50421081-50421082
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:50419009..50422090-chr3:50424618..50428241,4	MCF-7	breast:
2	chr3:50420263..50421916-chr3:50428504..50431466,2	K562	blood:
3	chr3:50420710..50423893-chr3:50432080..50434789,3	MCF-7	breast:

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1107265	0.86[ASW][hapmap];0.91[MEX][hapmap];0.85[YRI][hapmap];0.81[AMR][1000 genomes]
rs12494414	0.81[CHD][hapmap];0.83[JPT][hapmap]
rs12494849	0.86[ASW][hapmap]
rs12629572	0.93[CHD][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs1467914	0.86[ASW][hapmap]
rs1989839	0.89[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs2073496	0.81[AMR][1000 genomes]
rs2073499	0.86[ASW][hapmap];0.89[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2233474	0.93[ASW][hapmap];0.89[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2236948	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2236949	0.87[CHB][hapmap];0.83[JPT][hapmap]
rs2236950	0.95[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2236954	0.85[YRI][hapmap];0.82[AMR][1000 genomes]
rs2236957	0.82[AMR][1000 genomes]
rs2236959	0.85[YRI][hapmap]
rs2236964	0.86[ASW][hapmap];0.91[MEX][hapmap];0.85[YRI][hapmap];0.81[AMR][1000 genomes]
rs2236965	0.86[ASW][hapmap];0.87[MEX][hapmap];0.82[YRI][hapmap];0.81[AMR][1000 genomes]
rs2236973	0.86[ASW][hapmap];0.87[MEX][hapmap];0.89[YRI][hapmap];0.81[AMR][1000 genomes]
rs2236979	0.86[ASW][hapmap];0.87[MEX][hapmap];0.85[YRI][hapmap]
rs2236984	0.86[ASW][hapmap];0.83[MEX][hapmap];0.85[YRI][hapmap]
rs2236987	0.86[ASW][hapmap];0.87[MEX][hapmap];0.85[YRI][hapmap]
rs2282751	0.89[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap]
rs2282752	0.85[YRI][hapmap];0.82[AMR][1000 genomes]
rs2282753	0.86[ASW][hapmap];0.91[MEX][hapmap];0.85[YRI][hapmap];0.82[AMR][1000 genomes]
rs2282754	0.91[MEX][hapmap]
rs2282762	0.81[AMR][1000 genomes]
rs2298955	0.87[MEX][hapmap]
rs4141060	0.89[CHB][hapmap];0.90[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap]
rs57838764	0.88[ASN][1000 genomes]
rs6776145	0.89[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs734767	0.91[MEX][hapmap];0.85[YRI][hapmap];0.82[AMR][1000 genomes]
rs739431	0.81[GIH][hapmap]
rs743756	0.86[ASW][hapmap];0.87[MEX][hapmap];0.85[YRI][hapmap]
rs743757	0.86[ASW][hapmap];0.91[MEX][hapmap];0.85[YRI][hapmap];0.81[AMR][1000 genomes]
rs743857	0.86[ASW][hapmap];0.83[MEX][hapmap];0.85[YRI][hapmap]
rs9835537	0.86[ASW][hapmap];0.87[MEX][hapmap];0.85[YRI][hapmap]
rs9852677	0.81[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv523662	chr3:50144951-50584999	Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
2	esv1821728	chr3:50156142-50657253	Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
3	esv1793751	chr3:50157364-50476363	Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
4	esv1828162	chr3:50157364-50506151	Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
5	nsv470561	chr3:50158774-50584999	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
6	nsv876770	chr3:50158774-50609624	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
7	nsv1001993	chr3:50187646-50640808	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
8	nsv460531	chr3:50247824-50436827	Strong transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
9	nsv590255	chr3:50247824-50436827	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
10	nsv876772	chr3:50255305-50436827	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
11	nsv876774	chr3:50302830-50436827	Enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
12	nsv876773	chr3:50302830-50480131	Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
13	nsv834693	chr3:50302830-50507964	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
14	nsv876775	chr3:50324672-50504896	Flanking Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
15	esv3584502	chr3:50368278-50659741	Strong transcription Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
16	nsv432419	chr3:50388396-50637496	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
17	nsv876778	chr3:50413707-50465518	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
18	nsv590271	chr3:50420554-50436716	Weak transcription Bivalent Enhancer Enhancers Genic enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats	Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2236951	TRAIP	cis	parietal	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50408800-50423800	Weak transcription	Fetal Brain Female	brain
2	chr3:50411400-50422600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr3:50411400-50430000	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr3:50412800-50428000	Weak transcription	Right Ventricle	heart
5	chr3:50415200-50428400	Weak transcription	Brain Anterior Caudate	brain
6	chr3:50416000-50421200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr3:50417000-50428000	Weak transcription	Gastric	stomach
8	chr3:50417600-50421400	Enhancers	Fetal Muscle Leg	muscle
9	chr3:50418200-50421600	Enhancers	Fetal Muscle Trunk	muscle
10	chr3:50419200-50421400	Enhancers	Fetal Kidney	kidney
11	chr3:50419600-50421600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
12	chr3:50419600-50426200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr3:50420000-50421400	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr3:50420200-50421800	Enhancers	Spleen	Spleen
15	chr3:50420200-50422400	Enhancers	Brain Inferior Temporal Lobe	brain
16	chr3:50420200-50423000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr3:50420400-50421200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr3:50420400-50422200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr3:50420400-50423600	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr3:50420600-50421600	Strong transcription	Fetal Intestine Small	intestine
21	chr3:50420600-50422200	Weak transcription	Fetal Stomach	stomach
22	chr3:50420600-50422600	Weak transcription	Fetal Brain Male	brain
23	chr3:50420600-50425200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr3:50420800-50421200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr3:50421000-50421200	Enhancers	Brain Germinal Matrix	brain
26	chr3:50421000-50421400	Enhancers	Esophagus	oesophagus
27	chr3:50421000-50421800	Enhancers	NHEK	skin
28	chr3:50421000-50422200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr3:50421000-50422600	Strong transcription	Lung	lung

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