Variant report

Variant	rs1114630
Chromosome Location	chr3:133094559-133094560
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	RAD21	chr3:133093971-133097201	SK-N-SH	brain:	n/a	chr3:133097180-133097193

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:132760283..132761204-chr3:133094502..133095134,2	MCF-7	breast:

Variant related genes	Relation type
TMEM108	TF binding region
ENSG00000144868	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1109858	0.82[JPT][hapmap]
rs1197287	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1197288	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1197293	0.85[CHB][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs1197296	1.00[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.98[ASN][1000 genomes]
rs1197297	0.91[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs1197298	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1197299	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1197301	0.90[ASN][1000 genomes]
rs1197302	0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap];0.93[ASN][1000 genomes]
rs1197304	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1197305	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1197306	0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1197308	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs1197309	0.95[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1197313	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1197314	0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1201671	0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1201673	0.91[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs12631678	0.91[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs1619552	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1619622	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1708376	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1708377	0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1708384	0.88[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1708385	0.87[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs1795101	0.82[JPT][hapmap]
rs1795104	0.93[ASN][1000 genomes]
rs1795107	0.95[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2089987	0.83[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs2670179	0.95[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2699880	0.83[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs2699882	0.95[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap];0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs3732572	0.87[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs4854583	0.89[ASN][1000 genomes]
rs4854719	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.90[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4854720	0.83[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs56181416	0.86[ASN][1000 genomes]
rs656721	0.81[CHD][hapmap];0.95[JPT][hapmap]
rs6780144	0.92[ASN][1000 genomes]
rs6802663	0.87[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs938229	0.86[TSI][hapmap]
rs938230	0.86[CHD][hapmap]
rs938231	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9850193	0.82[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs9853752	0.96[ASN][1000 genomes]
rs9853757	0.96[ASN][1000 genomes]

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	nsv877503	chr3:133035774-133104631	Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1114630	RAB6B	cis	parietal	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:133080800-133098600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr3:133083200-133099200	Weak transcription	Lung	lung
3	chr3:133089200-133094800	Weak transcription	Fetal Lung	lung
4	chr3:133092400-133096400	Enhancers	Cortex derived primary cultured neurospheres	brain
5	chr3:133092600-133096400	Enhancers	Fetal Brain Male	brain
6	chr3:133092800-133095000	Enhancers	HUES64 Cell Line	embryonic stem cell
7	chr3:133093000-133094800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr3:133093000-133094800	Enhancers	iPS-18 Cell Line	embryonic stem cell
9	chr3:133093000-133095200	Enhancers	HUES48 Cell Line	embryonic stem cell
10	chr3:133093000-133102400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr3:133093600-133094800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr3:133093600-133094800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
13	chr3:133093600-133095000	Enhancers	HUES6 Cell Line	embryonic stem cell
14	chr3:133093800-133094800	Enhancers	iPS-15b Cell Line	embryonic stem cell
15	chr3:133093800-133094800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr3:133093800-133095000	Enhancers	ES-I3 Cell Line	embryonic stem cell
17	chr3:133093800-133095000	Enhancers	H1 Cell Line	embryonic stem cell
18	chr3:133093800-133095000	Enhancers	H9 Cell Line	embryonic stem cell
19	chr3:133093800-133096400	Enhancers	Fetal Brain Female	brain
20	chr3:133093800-133098200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr3:133094000-133094800	Enhancers	iPS-20b Cell Line	embryonic stem cell
22	chr3:133094000-133099400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr3:133094000-133099800	Weak transcription	HSMMtube	muscle
24	chr3:133094000-133109000	Weak transcription	HSMM	muscle
25	chr3:133094200-133095200	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr3:133094200-133096000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr3:133094200-133096000	Enhancers	Brain Germinal Matrix	brain
28	chr3:133094200-133100000	Weak transcription	Brain Hippocampus Middle	brain
29	chr3:133094400-133094800	Weak transcription	Brain Cingulate Gyrus	brain
30	chr3:133094400-133096200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr3:133094400-133100000	Weak transcription	Brain Angular Gyrus	brain
32	chr3:133094400-133102800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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