Variant report

Variant	rs11896713
Chromosome Location	chr2:134257724-134257725
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:134257170..134260161-chr2:134313651..134315459,2	MCF-7	breast:
2	chr2:134245342..134247871-chr2:134256827..134259265,2	MCF-7	breast:
3	chr2:134253868..134259578-chr2:134259579..134266138,12	MCF-7	breast:

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1008125	0.95[CEU][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1017368	0.95[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.89[ASN][1000 genomes]
rs11695605	0.88[CEU][hapmap];0.90[CHB][hapmap];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1836671	0.83[CHB][hapmap]
rs1865585	0.92[CEU][hapmap];0.93[GIH][hapmap];0.82[MEX][hapmap];0.86[MKK][hapmap];0.84[TSI][hapmap];0.92[EUR][1000 genomes]
rs1897429	0.92[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];0.80[JPT][hapmap];0.85[MKK][hapmap];0.90[TSI][hapmap];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2163653	0.91[EUR][1000 genomes]
rs2163654	0.92[CEU][hapmap];0.81[GIH][hapmap];0.84[MKK][hapmap];0.81[TSI][hapmap];0.93[EUR][1000 genomes]
rs2320935	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2874399	0.92[CEU][hapmap];0.93[GIH][hapmap];0.80[JPT][hapmap];0.82[MEX][hapmap];0.87[TSI][hapmap];0.92[EUR][1000 genomes]
rs3910163	0.92[CEU][hapmap];0.91[CHB][hapmap];0.80[JPT][hapmap];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4953883	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs4954052	0.89[EUR][1000 genomes]
rs4954059	0.81[CEU][hapmap];0.83[MKK][hapmap];0.81[EUR][1000 genomes]
rs7559239	0.95[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs7595258	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv997821	chr2:133868822-134360220	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv535927	chr2:133868822-134360220	Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv1002488	chr2:133890159-134275312	Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv535928	chr2:133890159-134275312	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv1003624	chr2:134126928-134583203	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11896713	RAB3GAP1	cis	parietal	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:134240000-134262400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr2:134246400-134262400	Weak transcription	Gastric	stomach
3	chr2:134248000-134262000	Weak transcription	NHLF	lung
4	chr2:134250800-134257800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr2:134251600-134261400	Weak transcription	Right Atrium	heart
6	chr2:134255000-134258200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr2:134255400-134259800	Weak transcription	Left Ventricle	heart
8	chr2:134255400-134261800	Weak transcription	Brain Anterior Caudate	brain
9	chr2:134255400-134261800	Weak transcription	Brain Cingulate Gyrus	brain
10	chr2:134255400-134262000	Weak transcription	Brain Angular Gyrus	brain
11	chr2:134255400-134262200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr2:134255600-134260400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr2:134255800-134258600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr2:134255800-134260200	Weak transcription	Brain Hippocampus Middle	brain
15	chr2:134255800-134260400	Weak transcription	Liver	Liver
16	chr2:134255800-134260600	Weak transcription	Brain Substantia Nigra	brain
17	chr2:134256600-134258400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr2:134256600-134258800	Enhancers	NHEK	skin
19	chr2:134256600-134261800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr2:134256600-134262000	Weak transcription	Fetal Lung	lung
21	chr2:134256600-134262200	Weak transcription	Fetal Stomach	stomach
22	chr2:134256600-134262400	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr2:134256800-134261200	Weak transcription	Duodenum Mucosa	Duodenum
24	chr2:134256800-134262200	Weak transcription	Fetal Brain Male	brain
25	chr2:134257000-134258200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr2:134257000-134258400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr2:134257000-134258800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr2:134257000-134260400	Weak transcription	Small Intestine	intestine
29	chr2:134257000-134261400	Weak transcription	Fetal Brain Female	brain
30	chr2:134257000-134262000	Weak transcription	Fetal Kidney	kidney
31	chr2:134257200-134259800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr2:134257200-134260200	Weak transcription	Fetal Intestine Small	intestine
33	chr2:134257200-134260400	Weak transcription	Stomach Mucosa	stomach
34	chr2:134257200-134262000	Weak transcription	Brain Germinal Matrix	brain
35	chr2:134257200-134262400	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr2:134257400-134257800	Weak transcription	NHDF-Ad	bronchial
37	chr2:134257400-134262400	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr2:134257600-134257800	Weak transcription	HMEC	breast
39	chr2:134257600-134258000	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr2:134257600-134260400	Weak transcription	Fetal Intestine Large	intestine

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