Variant report

Variant	rs10800477
Chromosome Location	chr1:169761107-169761108
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:169760980-169761319	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr1:169760992-169761267	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr1:169759589-169761500	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:169732129..169734775-chr1:169760977..169762704,2	K562	blood:
2	chr1:169755971..169761352-chr1:169761713..169764832,7	MCF-7	breast:

Variant related genes	Relation type
C1orf112	TF binding region
ENSG00000007908	Chromatin interaction
ENSG00000171806	Chromatin interaction
ENSG00000000460	Chromatin interaction
ENSG00000230704	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10159425	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10489170	1.00[CEU][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];0.94[EUR][1000 genomes]
rs10489177	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10753796	0.93[CHB][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs10753798	0.81[CHB][hapmap]
rs10800478	0.81[CHB][hapmap]
rs10800482	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10919243	0.87[CHB][hapmap]
rs10919260	1.00[CEU][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];0.94[EUR][1000 genomes]
rs10919270	0.85[CEU][hapmap];0.91[MEX][hapmap]
rs10919271	0.85[CEU][hapmap]
rs10919272	0.85[CEU][hapmap];0.91[MEX][hapmap]
rs11804170	0.85[CEU][hapmap]
rs12049325	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12127655	0.82[MEX][hapmap]
rs12128754	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12135656	0.90[ASW][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];0.83[JPT][hapmap];0.92[LWK][hapmap];0.84[MEX][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs12135826	0.94[EUR][1000 genomes]
rs12138675	1.00[CEU][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];0.94[EUR][1000 genomes]
rs12401338	0.80[EUR][1000 genomes]
rs12760433	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2143121	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2272916	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3753311	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs6427223	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6427229	0.91[MEX][hapmap]
rs6658548	0.94[EUR][1000 genomes]
rs6670253	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6679646	1.00[CEU][hapmap];0.81[JPT][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6688806	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs7533194	0.80[EUR][1000 genomes]
rs7552710	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs882595	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.88[TSI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9787237	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9803717	0.81[CHB][hapmap]
rs9803860	0.81[CHB][hapmap]

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	esv3451367	chr1:169630075-169976964	Strong transcription Flanking Active TSS Genic enhancers Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10800477	C1orf156	cis	cerebellum	SCAN
rs10800477	LMX1A	cis	parietal	SCAN
rs10800477	CREG1	cis	cerebellum	SCAN
rs10800477	C1orf112	cis	cerebellum	SCAN

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169749400-169761400	Weak transcription	Liver	Liver
2	chr1:169750800-169762800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr1:169751600-169762600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr1:169753600-169763000	Weak transcription	HMEC	breast
5	chr1:169756400-169762400	Weak transcription	Fetal Brain Male	brain
6	chr1:169756600-169762600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr1:169757000-169762400	Weak transcription	Fetal Thymus	thymus
8	chr1:169757400-169763000	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr1:169757400-169763000	Weak transcription	Thymus	Thymus
10	chr1:169757400-169763200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr1:169757600-169762200	Weak transcription	Fetal Intestine Small	intestine
12	chr1:169757600-169763000	Weak transcription	Monocytes-CD14+_RO01746	blood
13	chr1:169758000-169762800	Weak transcription	Primary B cells from cord blood	blood
14	chr1:169758200-169761200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr1:169758200-169763200	Weak transcription	Adipose Nuclei	Adipose
16	chr1:169758200-169763200	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr1:169758400-169761600	Weak transcription	HepG2	liver
18	chr1:169758600-169763000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr1:169758600-169763200	Weak transcription	Brain Hippocampus Middle	brain
20	chr1:169758600-169763200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr1:169758600-169763400	Weak transcription	Gastric	stomach
22	chr1:169758800-169762200	Weak transcription	Aorta	Aorta
23	chr1:169758800-169762400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr1:169758800-169763000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr1:169758800-169763000	Weak transcription	Rectal Smooth Muscle	rectum
26	chr1:169758800-169763200	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr1:169758800-169763200	Weak transcription	HSMM	muscle
28	chr1:169758800-169763600	Weak transcription	Spleen	Spleen
29	chr1:169759000-169762600	Weak transcription	Brain Germinal Matrix	brain
30	chr1:169759000-169762800	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr1:169759000-169763000	Weak transcription	Duodenum Mucosa	Duodenum
32	chr1:169759000-169763000	Weak transcription	A549	lung
33	chr1:169759200-169761400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr1:169759200-169763000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr1:169759200-169763200	Weak transcription	Ovary	ovary
36	chr1:169759200-169763200	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr1:169759400-169762600	Weak transcription	Brain Anterior Caudate	brain
38	chr1:169759400-169763000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr1:169759600-169763000	Weak transcription	Brain Substantia Nigra	brain
40	chr1:169759600-169763200	Weak transcription	Pancreas	Pancrea
41	chr1:169759800-169763200	Weak transcription	Fetal Intestine Large	intestine
42	chr1:169759800-169763200	Weak transcription	Stomach Smooth Muscle	stomach
43	chr1:169760000-169761400	Strong transcription	Rectal Mucosa Donor 29	rectum
44	chr1:169760000-169763000	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr1:169760200-169761600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
46	chr1:169760200-169763000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr1:169760400-169761200	Weak transcription	Fetal Muscle Trunk	muscle
48	chr1:169760400-169761600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr1:169760400-169761800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
50	chr1:169760400-169762000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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