Variant report

Variant	rs1063729
Chromosome Location	chr2:169630483-169630484
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:4)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:169628746..169631542-chr2:169795260..169797198,2	K562	blood:
2	chr2:169630126..169630739-chr7:14783533..14784033,2	MCF-7	breast:
3	chr2:169629191..169630841-chr2:169776722..169777731,4	MCF-7	breast:
4	chr2:169629920..169631115-chr2:169776779..169777787,11	K562	blood:
5	chr2:169630102..169630887-chr2:169804877..169805660,3	MCF-7	breast:
6	chr2:169629983..169630659-chr2:169997990..169998500,2	K562	blood:
7	chr2:169629254..169632077-chr2:169708619..169710261,2	K562	blood:
8	chr2:169621495..169622271-chr2:169629860..169630520,3	K562	blood:
9	chr2:169629519..169633434-chr2:169651628..169656188,4	K562	blood:
10	chr2:169624850..169627444-chr2:169628173..169630691,3	K562	blood:
11	chr2:169614606..169616373-chr2:169628281..169631112,2	K562	blood:
12	chr2:169629906..169631239-chr2:169776809..169777837,8	MCF-7	breast:
13	chr2:169630347..169631099-chr20:6143956..6144677,2	MCF-7	breast:

(count:4 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SPC25-1	chr2:169628463-169631148	ENSG00000227617.2
2	lnc-SPC25-1	chr2:169628461-169631148	NONHSAT075331
3	lnc-SPC25-1	chr2:169628461-169631148	NONHSAT075332
4	lnc-SPC25-1	chr2:169628464-169631148	NONHSAT075333

No data

Variant related genes	Relation type
ENSG00000163072	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10197317	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12692886	0.86[MEX][hapmap]
rs12692887	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16855886	0.82[CHB][hapmap]
rs16855893	0.82[CHB][hapmap]
rs3732030	0.91[CHB][hapmap]
rs3843327	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3914919	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs57805112	0.93[ASN][1000 genomes]
rs61386309	0.87[ASN][1000 genomes]
rs6433090	0.85[ASN][1000 genomes]
rs6433091	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7584527	0.87[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.85[TSI][hapmap];0.85[ASN][1000 genomes]
rs9287901	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[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	nsv915920	chr2:168851960-169696591	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1063729	C2orf77	cis	cerebellum	SCAN

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:169579600-169630600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr2:169597200-169635800	Weak transcription	Ovary	ovary
3	chr2:169606000-169630600	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr2:169606000-169630600	Weak transcription	Adipose Nuclei	Adipose
5	chr2:169606600-169630600	Weak transcription	Gastric	stomach
6	chr2:169606600-169632800	Weak transcription	Pancreas	Pancrea
7	chr2:169608200-169633800	Weak transcription	Psoas Muscle	Psoas
8	chr2:169608400-169632200	Weak transcription	HSMMtube	muscle
9	chr2:169608400-169633600	Weak transcription	Dnd41	blood
10	chr2:169609200-169636400	Weak transcription	Lung	lung
11	chr2:169609400-169633000	Weak transcription	Rectal Smooth Muscle	rectum
12	chr2:169609600-169634200	Weak transcription	Fetal Brain Male	brain
13	chr2:169610000-169630600	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr2:169610800-169637400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr2:169611200-169636600	Weak transcription	HepG2	liver
16	chr2:169614400-169631800	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr2:169615800-169630600	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr2:169621600-169631000	Strong transcription	Fetal Thymus	thymus
19	chr2:169622200-169641400	Weak transcription	Small Intestine	intestine
20	chr2:169622400-169631400	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr2:169623400-169630600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr2:169623400-169632600	Weak transcription	Right Ventricle	heart
23	chr2:169623400-169632800	Weak transcription	Primary neutrophils fromperipheralblood	blood
24	chr2:169624200-169630600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr2:169624400-169632800	Weak transcription	NHEK	skin
26	chr2:169624800-169632200	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr2:169625400-169633000	Strong transcription	Primary T cells from cord blood	blood
28	chr2:169625600-169632400	Weak transcription	Fetal Intestine Small	intestine
29	chr2:169625600-169635400	Weak transcription	Fetal Stomach	stomach
30	chr2:169626400-169632200	Weak transcription	GM12878-XiMat	blood
31	chr2:169626600-169630600	Weak transcription	Primary T helper cells PMA-I stimulated	--
32	chr2:169626600-169632000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr2:169626600-169632200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr2:169626600-169632200	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr2:169626600-169632400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr2:169626600-169632400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr2:169626600-169632400	Weak transcription	Duodenum Mucosa	Duodenum
38	chr2:169626600-169632600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr2:169626800-169631200	Enhancers	Fetal Heart	heart
40	chr2:169626800-169632000	Weak transcription	Fetal Muscle Leg	muscle
41	chr2:169626800-169633000	Weak transcription	Primary B cells from cord blood	blood
42	chr2:169626800-169633800	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr2:169626800-169641800	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr2:169627000-169632400	Weak transcription	Stomach Smooth Muscle	stomach
45	chr2:169627200-169632000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr2:169627400-169632400	Weak transcription	Primary hematopoietic stem cells	blood
47	chr2:169627600-169631400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr2:169627600-169632400	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr2:169627800-169632400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr2:169627800-169636600	Weak transcription	Fetal Kidney	kidney

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