Variant report

Variant	rs12679938
Chromosome Location	chr8:59498685-59498686
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:59488834..59491780-chr8:59497292..59499842,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000137575	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10091952	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10092359	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10094910	0.89[EUR][1000 genomes]
rs10099153	0.81[EUR][1000 genomes]
rs10099912	0.81[EUR][1000 genomes]
rs10100873	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10102709	0.90[TSI][hapmap]
rs10104292	0.87[CEU][hapmap];0.81[GIH][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs10106272	0.93[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10107530	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10110065	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10110111	0.80[AMR][1000 genomes]
rs10111052	0.84[CEU][hapmap];0.89[EUR][1000 genomes]
rs10111180	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs10113323	0.91[CEU][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10113667	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10113750	0.88[TSI][hapmap]
rs10113830	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10504256	0.87[CEU][hapmap];0.82[EUR][1000 genomes]
rs1050488	0.87[GIH][hapmap];0.82[JPT][hapmap];0.93[MEX][hapmap];0.92[TSI][hapmap];0.88[AMR][1000 genomes]
rs1050504	0.89[GIH][hapmap];0.82[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11774558	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11775194	0.82[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11782455	0.87[CEU][hapmap];0.82[JPT][hapmap];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11783174	0.82[EUR][1000 genomes]
rs11785141	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12674568	0.90[TSI][hapmap]
rs12674724	0.92[EUR][1000 genomes]
rs12676593	0.81[EUR][1000 genomes]
rs12677290	0.87[CEU][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes]
rs12678669	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12680996	0.88[TSI][hapmap]
rs1352496	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1387222	0.81[GIH][hapmap]
rs16923588	0.82[EUR][1000 genomes]
rs16923594	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs17206746	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17263989	0.80[AMR][1000 genomes]
rs17272151	1.00[CEU][hapmap];0.88[GIH][hapmap];0.93[MEX][hapmap];0.87[MKK][hapmap];0.92[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1976162	0.87[CEU][hapmap];0.82[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2130072	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2279460	0.87[CEU][hapmap];0.87[TSI][hapmap];0.88[EUR][1000 genomes]
rs2279462	0.87[CEU][hapmap];0.89[EUR][1000 genomes]
rs28656336	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs28711402	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28809811	0.85[EUR][1000 genomes]
rs3816846	0.87[CEU][hapmap];0.89[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4400366	0.82[EUR][1000 genomes]
rs4579515	0.87[CEU][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs4598239	0.88[GIH][hapmap];0.84[TSI][hapmap]
rs56249776	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs59979442	0.81[EUR][1000 genomes]
rs6981601	0.88[TSI][hapmap]
rs6991020	0.83[EUR][1000 genomes]
rs6995115	0.87[CEU][hapmap];0.83[EUR][1000 genomes]
rs72647424	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72647425	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs72647434	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs72647437	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72647443	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7825739	0.88[GIH][hapmap];0.84[TSI][hapmap]
rs7825996	0.80[EUR][1000 genomes]
rs7826122	0.87[CEU][hapmap];0.80[EUR][1000 genomes]
rs7840932	0.82[EUR][1000 genomes]
rs7844231	0.87[CEU][hapmap];0.81[EUR][1000 genomes]
rs8192870	0.88[CHB][hapmap];0.83[CHD][hapmap];0.81[MEX][hapmap]
rs9297996	0.82[EUR][1000 genomes]
rs9297997	0.86[TSI][hapmap]
rs9297998	0.87[CEU][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes]
rs9297999	0.89[GIH][hapmap];0.82[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv890938	chr8:59355053-59809785	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv890939	chr8:59471187-59544413	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases
3	nsv1031537	chr8:59482949-59536971	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases
4	nsv831325	chr8:59492580-59694443	Genic enhancers Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12679938	RAB2A	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:59467400-59559400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr8:59472800-59515800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr8:59473000-59506400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr8:59473200-59508600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr8:59476600-59505600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr8:59476800-59500600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr8:59477000-59508200	Strong transcription	HUES64 Cell Line	embryonic stem cell
8	chr8:59477200-59503000	Strong transcription	Primary neutrophils fromperipheralblood	blood
9	chr8:59477200-59503400	Strong transcription	NHDF-Ad	bronchial
10	chr8:59477200-59506200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
11	chr8:59477600-59500600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr8:59477600-59503600	Strong transcription	Osteobl	bone
13	chr8:59477600-59514200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr8:59477800-59508800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr8:59478000-59500400	Strong transcription	NH-A	brain
16	chr8:59478000-59500800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr8:59478000-59502800	Strong transcription	Fetal Thymus	thymus
18	chr8:59478000-59503000	Strong transcription	Muscle Satellite Cultured Cells	--
19	chr8:59478000-59503200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr8:59478000-59506400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr8:59478000-59508200	Strong transcription	Primary B cells from peripheral blood	blood
22	chr8:59478000-59508600	Strong transcription	Primary T helper cells fromperipheralblood	blood
23	chr8:59478000-59508800	Strong transcription	Fetal Intestine Large	intestine
24	chr8:59479000-59503800	Strong transcription	Rectal Mucosa Donor 29	rectum
25	chr8:59479200-59499400	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr8:59479200-59505600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr8:59479600-59500600	Strong transcription	HUVEC	blood vessel
28	chr8:59479600-59508000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr8:59480400-59503000	Strong transcription	Adipose Nuclei	Adipose
30	chr8:59480600-59515800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr8:59481400-59502000	Weak transcription	Fetal Brain Male	brain
32	chr8:59483000-59504400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr8:59483200-59508800	Strong transcription	Primary T cells fromperipheralblood	blood
34	chr8:59483400-59501000	Strong transcription	Primary B cells from cord blood	blood
35	chr8:59483800-59500600	Strong transcription	Liver	Liver
36	chr8:59483800-59500600	Strong transcription	Skeletal Muscle Female	skeletal muscle
37	chr8:59483800-59504400	Strong transcription	Duodenum Mucosa	Duodenum
38	chr8:59483800-59528000	Strong transcription	Dnd41	blood
39	chr8:59484000-59505600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr8:59484400-59503200	Strong transcription	HUES6 Cell Line	embryonic stem cell
41	chr8:59484400-59503800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr8:59484800-59502600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr8:59484800-59503200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
44	chr8:59484800-59505600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr8:59485200-59500400	Strong transcription	Cortex derived primary cultured neurospheres	brain
46	chr8:59485400-59501600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr8:59485600-59500400	Strong transcription	Fetal Brain Female	brain
48	chr8:59485800-59500000	Strong transcription	A549	lung
49	chr8:59487400-59500600	Strong transcription	Left Ventricle	heart
50	chr8:59487400-59500800	Strong transcription	Hela-S3	cervix

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