Variant report

Variant	rs17200336
Chromosome Location	chr8:104064165-104064166
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	chr8:104032214..104034856-chr8:104064086..104065611,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000155097	Chromatin interaction
ENSG00000254236	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10099825	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13271522	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2015790	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2270673	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2515198	0.88[CEU][hapmap];0.94[CHB][hapmap];0.83[ASN][1000 genomes]
rs2515200	0.83[ASW][hapmap]
rs28460720	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35242416	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3779909	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4147529	0.81[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.90[YRI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4734068	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4734683	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4734684	0.81[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs868936	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9283939	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.90[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[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	esv33118	chr8:103358567-104068172	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	145 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17200336	CTHRC1	cis	cerebellum	SCAN
rs17200336	ATP6V1C1	cis	cerebellum	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:104034200-104068800	Weak transcription	Small Intestine	intestine
2	chr8:104034400-104069400	Weak transcription	Esophagus	oesophagus
3	chr8:104034600-104068400	Weak transcription	Right Ventricle	heart
4	chr8:104034800-104065600	Weak transcription	Fetal Kidney	kidney
5	chr8:104034800-104074600	Weak transcription	NHEK	skin
6	chr8:104035400-104071200	Weak transcription	Brain Angular Gyrus	brain
7	chr8:104036200-104065200	Weak transcription	Colon Smooth Muscle	Colon
8	chr8:104037200-104071400	Weak transcription	Fetal Brain Female	brain
9	chr8:104038000-104066800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr8:104039000-104069400	Weak transcription	Spleen	Spleen
11	chr8:104040200-104071400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr8:104040600-104071400	Weak transcription	Pancreas	Pancrea
13	chr8:104043800-104068200	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr8:104044000-104066400	Weak transcription	HMEC	breast
15	chr8:104046000-104068000	Weak transcription	NHLF	lung
16	chr8:104050400-104069200	Weak transcription	Aorta	Aorta
17	chr8:104050400-104086000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr8:104050600-104066600	Weak transcription	Ovary	ovary
19	chr8:104050600-104089600	Weak transcription	Psoas Muscle	Psoas
20	chr8:104050800-104067800	Weak transcription	Brain Substantia Nigra	brain
21	chr8:104050800-104069800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr8:104051600-104087400	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr8:104052600-104065400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr8:104052600-104066600	Strong transcription	Primary monocytes fromperipheralblood	blood
25	chr8:104052800-104082200	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr8:104053000-104066800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr8:104053000-104067000	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr8:104053000-104068600	Strong transcription	Duodenum Smooth Muscle	Duodenum
29	chr8:104053200-104073000	Weak transcription	Colonic Mucosa	Colon
30	chr8:104053200-104085600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr8:104053600-104083800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr8:104053800-104067600	Strong transcription	Primary B cells from cord blood	blood
33	chr8:104054000-104084400	Strong transcription	Fetal Thymus	thymus
34	chr8:104054200-104083400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr8:104054200-104083800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
36	chr8:104054200-104084400	Strong transcription	Primary B cells from peripheral blood	blood
37	chr8:104055000-104065000	Weak transcription	Brain Cingulate Gyrus	brain
38	chr8:104055200-104087000	Weak transcription	K562	blood
39	chr8:104055400-104069800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr8:104056200-104077000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr8:104056800-104066200	Weak transcription	Fetal Brain Male	brain
42	chr8:104056800-104069400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr8:104057000-104084200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr8:104057400-104065400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr8:104058400-104067400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr8:104058400-104068000	Weak transcription	Fetal Heart	heart
47	chr8:104058800-104071600	Strong transcription	HSMM	muscle
48	chr8:104058800-104073600	Strong transcription	Dnd41	blood
49	chr8:104058800-104083400	Strong transcription	Rectal Mucosa Donor 29	rectum
50	chr8:104059000-104067800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

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