Variant report

Variant	rs7559239
Chromosome Location	chr2:134253973-134253974
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	chr2:134253868..134259578-chr2:134259579..134266138,12	MCF-7	breast:
2	chr2:134248085..134250298-chr2:134253580..134256578,3	MCF-7	breast:

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1008125	0.91[CEU][hapmap];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1017368	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11695605	0.82[CEU][hapmap];0.95[CHB][hapmap];0.83[JPT][hapmap];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11887480	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11896713	0.95[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs1836671	0.82[CEU][hapmap];0.87[CHB][hapmap];0.86[MEX][hapmap];0.85[MKK][hapmap];0.86[TSI][hapmap];0.84[YRI][hapmap]
rs1865585	0.85[CEU][hapmap];0.81[CHD][hapmap];0.98[GIH][hapmap];0.83[EUR][1000 genomes]
rs1897429	0.85[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];0.83[TSI][hapmap];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2163653	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2320935	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2874399	0.85[CEU][hapmap];0.86[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];0.81[TSI][hapmap];0.84[EUR][1000 genomes]
rs3910163	0.85[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4953883	0.82[CEU][hapmap];0.87[CHB][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.84[YRI][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4954052	0.81[EUR][1000 genomes]
rs7595258	0.81[EUR][1000 genomes];0.94[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
rs7559239	RAB3GAP1	cis	parietal	SCAN

Chromatin state (count:42 , 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	chr2:134247800-134254800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr2:134248000-134262000	Weak transcription	NHLF	lung
5	chr2:134248200-134256600	Weak transcription	NHEK	skin
6	chr2:134248400-134255000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr2:134249000-134254400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr2:134249000-134254600	Weak transcription	NHDF-Ad	bronchial
9	chr2:134250200-134257200	Enhancers	Fetal Intestine Small	intestine
10	chr2:134250400-134255800	Enhancers	Liver	Liver
11	chr2:134250800-134257800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr2:134251600-134254000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr2:134251600-134261400	Weak transcription	Right Atrium	heart
14	chr2:134252200-134254000	Enhancers	Duodenum Mucosa	Duodenum
15	chr2:134252200-134257000	Enhancers	Fetal Kidney	kidney
16	chr2:134252600-134254800	Enhancers	Brain Germinal Matrix	brain
17	chr2:134252600-134255800	Enhancers	Brain Substantia Nigra	brain
18	chr2:134252600-134257000	Enhancers	Fetal Brain Female	brain
19	chr2:134252600-134257600	Enhancers	Cortex derived primary cultured neurospheres	brain
20	chr2:134252800-134254000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr2:134252800-134254600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr2:134252800-134255400	Enhancers	Brain Anterior Caudate	brain
23	chr2:134252800-134255400	Enhancers	Brain Cingulate Gyrus	brain
24	chr2:134252800-134255600	Enhancers	Breast Myoepithelial Primary Cells	Breast
25	chr2:134252800-134255800	Enhancers	Brain Hippocampus Middle	brain
26	chr2:134253000-134254000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
27	chr2:134253200-134254600	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr2:134253200-134255000	Enhancers	Fetal Brain Male	brain
29	chr2:134253200-134255000	Weak transcription	Fetal Muscle Leg	muscle
30	chr2:134253200-134255000	Weak transcription	Left Ventricle	heart
31	chr2:134253200-134255200	Weak transcription	Stomach Mucosa	stomach
32	chr2:134253200-134255800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr2:134253400-134254600	Weak transcription	Brain Angular Gyrus	brain
34	chr2:134253400-134254800	Weak transcription	Fetal Stomach	stomach
35	chr2:134253400-134254800	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr2:134253400-134255400	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr2:134253600-134254000	Weak transcription	Fetal Lung	lung
38	chr2:134253600-134254200	Weak transcription	Fetal Intestine Large	intestine
39	chr2:134253800-134254000	Enhancers	Small Intestine	intestine
40	chr2:134253800-134254600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr2:134253800-134254800	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr2:134253800-134255800	Enhancers	HUES48 Cell Line	embryonic stem cell

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