Variant report

Variant	rs3779909
Chromosome Location	chr8:104054262-104054263
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	chr8:104046808..104050874-chr8:104051306..104055177,3	MCF-7	breast:

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10099825	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13271522	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17200336	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]
rs2015790	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2047378	0.82[YRI][hapmap]
rs2048550	0.82[YRI][hapmap]
rs2270673	1.00[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];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2515194	0.82[YRI][hapmap]
rs2515198	0.88[CEU][hapmap];0.94[CHB][hapmap];0.83[ASN][1000 genomes]
rs28460720	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35242416	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4147529	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4734068	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4734683	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4734684	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs868936	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9283939	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[MEX][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[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	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
rs3779909	CTHRC1	cis	cerebellum	SCAN
rs3779909	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	chr8:104034400-104059400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr8:104034400-104069400	Weak transcription	Esophagus	oesophagus
4	chr8:104034600-104059800	Weak transcription	A549	lung
5	chr8:104034600-104063600	Weak transcription	HSMMtube	muscle
6	chr8:104034600-104068400	Weak transcription	Right Ventricle	heart
7	chr8:104034800-104054400	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr8:104034800-104058800	Weak transcription	HSMM	muscle
9	chr8:104034800-104058800	Weak transcription	NH-A	brain
10	chr8:104034800-104065600	Weak transcription	Fetal Kidney	kidney
11	chr8:104034800-104074600	Weak transcription	NHEK	skin
12	chr8:104035400-104054600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr8:104035400-104061800	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr8:104035400-104071200	Weak transcription	Brain Angular Gyrus	brain
15	chr8:104035600-104054600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr8:104035600-104054600	Weak transcription	Stomach Smooth Muscle	stomach
17	chr8:104035800-104059400	Weak transcription	Thymus	Thymus
18	chr8:104035800-104061800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr8:104036000-104056600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr8:104036200-104065200	Weak transcription	Colon Smooth Muscle	Colon
21	chr8:104036800-104054600	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr8:104036800-104061200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr8:104037200-104063400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr8:104037200-104071400	Weak transcription	Fetal Brain Female	brain
25	chr8:104038000-104066800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr8:104038200-104054600	Weak transcription	K562	blood
27	chr8:104038400-104059400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr8:104038600-104059400	Weak transcription	Gastric	stomach
29	chr8:104039000-104069400	Weak transcription	Spleen	Spleen
30	chr8:104039800-104061200	Weak transcription	GM12878-XiMat	blood
31	chr8:104040200-104071400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr8:104040600-104071400	Weak transcription	Pancreas	Pancrea
33	chr8:104041000-104059200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr8:104042600-104054600	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr8:104043400-104056000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr8:104043800-104054800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr8:104043800-104068200	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr8:104044000-104054400	Weak transcription	HepG2	liver
39	chr8:104044000-104054800	Weak transcription	HUVEC	blood vessel
40	chr8:104044000-104056000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr8:104044000-104058400	Weak transcription	Fetal Intestine Small	intestine
42	chr8:104044000-104066400	Weak transcription	HMEC	breast
43	chr8:104046000-104068000	Weak transcription	NHLF	lung
44	chr8:104046400-104054800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
45	chr8:104048400-104063800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr8:104048600-104059400	Weak transcription	Lung	lung
47	chr8:104048800-104054800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr8:104049600-104059000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr8:104050200-104059200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr8:104050400-104069200	Weak transcription	Aorta	Aorta

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