Variant report

Variant	rs17035663
Chromosome Location	chr12:104892372-104892373
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:104892344..104895135-chr12:104897977..104900926,3	MCF-7	breast:
2	chr12:104889078..104893153-chr12:104897198..104902053,5	K562	blood:
3	chr12:104889682..104892508-chr12:104899984..104902053,3	K562	blood:
4	chr12:104850303..104852341-chr12:104891905..104894445,2	K562	blood:
5	chr12:104887555..104889139-chr12:104891204..104893677,2	K562	blood:

Variant related genes	Relation type
ENSG00000171310	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11608669	0.83[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11609491	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1882494	0.82[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2141855	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2141856	0.84[CHB][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4536299	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55778791	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56020814	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56138293	0.89[ASN][1000 genomes]
rs57525859	0.89[ASN][1000 genomes]
rs60351248	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7970489	0.95[ASN][1000 genomes]
rs7972097	0.82[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7972201	0.82[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832502	chr12:104833729-104908288	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv832504	chr12:104853331-105028245	Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
3	nsv868	chr12:104858964-104895572	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17035663	GOLGA2B	cis	cerebellum	SCAN
rs17035663	SCYL2	cis	parietal	SCAN

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104869200-104899600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr12:104873200-104895400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr12:104875200-104895400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr12:104875200-104897000	Weak transcription	NHEK	skin
5	chr12:104875400-104904200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr12:104879600-104893200	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr12:104880000-104893000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr12:104880000-104897800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr12:104880600-104897000	Weak transcription	Stomach Smooth Muscle	stomach
10	chr12:104881600-104898600	Weak transcription	A549	lung
11	chr12:104882600-104893200	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr12:104882600-104900600	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr12:104884200-104898000	Weak transcription	Gastric	stomach
14	chr12:104887200-104903000	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
15	chr12:104887600-104899400	Enhancers	Fetal Thymus	thymus
16	chr12:104888000-104897200	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr12:104888000-104900200	Weak transcription	Brain Substantia Nigra	brain
18	chr12:104888200-104893000	Weak transcription	Placenta	Placenta
19	chr12:104888200-104893400	Weak transcription	Rectal Smooth Muscle	rectum
20	chr12:104888200-104894600	Weak transcription	Esophagus	oesophagus
21	chr12:104888200-104896600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr12:104888400-104893600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr12:104888400-104895000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
24	chr12:104888800-104897000	Enhancers	Primary B cells from peripheral blood	blood
25	chr12:104888800-104898000	Weak transcription	Aorta	Aorta
26	chr12:104889000-104892400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
27	chr12:104889000-104892400	Enhancers	Primary T killer memory cells from peripheral blood	blood
28	chr12:104889000-104893000	Weak transcription	Colon Smooth Muscle	Colon
29	chr12:104889000-104894600	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr12:104889000-104895000	Enhancers	Primary T cells from cord blood	blood
31	chr12:104889000-104897400	Enhancers	Primary T cells fromperipheralblood	blood
32	chr12:104889200-104895000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
33	chr12:104889200-104898200	Weak transcription	HSMMtube	muscle
34	chr12:104889800-104899000	Weak transcription	Brain Anterior Caudate	brain
35	chr12:104890000-104895400	Weak transcription	NHDF-Ad	bronchial
36	chr12:104890000-104903800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr12:104890200-104896200	Enhancers	Primary hematopoietic stem cells	blood
38	chr12:104890400-104895600	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr12:104890400-104896600	Weak transcription	K562	blood
40	chr12:104890400-104898600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr12:104890400-104898800	Weak transcription	Brain Germinal Matrix	brain
42	chr12:104890600-104892600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
43	chr12:104890600-104893600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
44	chr12:104890600-104894000	Enhancers	Monocytes-CD14+_RO01746	blood
45	chr12:104890600-104894800	Enhancers	Primary monocytes fromperipheralblood	blood
46	chr12:104891000-104892400	Enhancers	Primary B cells from cord blood	blood
47	chr12:104891000-104893600	Weak transcription	Fetal Lung	lung
48	chr12:104891000-104893800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr12:104891200-104893000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr12:104891200-104893000	Weak transcription	Sigmoid Colon	Sigmoid Colon

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