Variant report

Variant	rs7535619
Chromosome Location	chr1:220404711-220404712
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:220403099..220406087-chr1:220921390..220923561,2	MCF-7	breast:
2	chr1:220403586..220405327-chr1:220408780..220410379,2	K562	blood:

Variant related genes	Relation type
ENSG00000117791	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10863537	0.83[CHB][hapmap];0.82[JPT][hapmap];0.95[YRI][hapmap]
rs10863538	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11118507	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12026681	1.00[CEU][hapmap];0.87[JPT][hapmap];0.88[EUR][1000 genomes]
rs1397958	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1588578	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2221833	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2667967	0.89[EUR][1000 genomes]
rs2667968	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2667969	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2667970	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2808008	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2808009	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2808011	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.96[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2808012	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2808013	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2808016	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2808018	1.00[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2808019	0.93[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.96[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2814492	0.95[ASN][1000 genomes]
rs2814494	0.82[ASN][1000 genomes]
rs2814495	0.94[ASN][1000 genomes]
rs4142940	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4511114	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6541127	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6696985	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[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	nsv4643	chr1:220397642-220442231	Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7535619	C1orf115	cis	lymphoblastoid	seeQTL
rs7535619	MOSC2	cis	lymphoblastoid	seeQTL

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:220374600-220407600	Weak transcription	Fetal Brain Male	brain
2	chr1:220379000-220418200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr1:220379200-220409600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr1:220379200-220410800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr1:220379200-220422600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr1:220381200-220422000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr1:220384200-220408800	Weak transcription	A549	lung
8	chr1:220384200-220420600	Weak transcription	Fetal Kidney	kidney
9	chr1:220384200-220423000	Weak transcription	Esophagus	oesophagus
10	chr1:220384200-220425800	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr1:220384400-220413400	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr1:220384800-220408000	Weak transcription	Hela-S3	cervix
13	chr1:220384800-220417000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr1:220385000-220405000	Weak transcription	Placenta	Placenta
15	chr1:220385400-220409000	Weak transcription	NH-A	brain
16	chr1:220385400-220419400	Weak transcription	HUVEC	blood vessel
17	chr1:220385600-220408000	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr1:220393000-220405400	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr1:220393000-220441000	Weak transcription	NHDF-Ad	bronchial
20	chr1:220393200-220408800	Weak transcription	Brain Angular Gyrus	brain
21	chr1:220393200-220413400	Weak transcription	Fetal Heart	heart
22	chr1:220393400-220405000	Weak transcription	Osteobl	bone
23	chr1:220393400-220411400	Weak transcription	Fetal Brain Female	brain
24	chr1:220393800-220425800	Weak transcription	Gastric	stomach
25	chr1:220394000-220422600	Weak transcription	Thymus	Thymus
26	chr1:220394400-220407800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr1:220398200-220406200	Strong transcription	Primary T cells from cord blood	blood
28	chr1:220398200-220406400	Strong transcription	Monocytes-CD14+_RO01746	blood
29	chr1:220398400-220420400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr1:220398600-220406400	Weak transcription	Brain Germinal Matrix	brain
31	chr1:220398800-220407000	Strong transcription	Primary monocytes fromperipheralblood	blood
32	chr1:220399000-220405400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr1:220399000-220405600	Weak transcription	Aorta	Aorta
34	chr1:220399000-220406200	Strong transcription	Primary B cells from cord blood	blood
35	chr1:220399000-220406800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr1:220399000-220407400	Weak transcription	Small Intestine	intestine
37	chr1:220399000-220418400	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr1:220399200-220405600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr1:220399200-220405600	Weak transcription	Brain Substantia Nigra	brain
40	chr1:220399200-220406200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr1:220399200-220414400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr1:220399400-220408200	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr1:220399600-220414600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr1:220400000-220406000	Strong transcription	Primary B cells from peripheral blood	blood
45	chr1:220400000-220406200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr1:220400200-220406200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr1:220400200-220406200	Strong transcription	Primary T cells fromperipheralblood	blood
48	chr1:220400400-220405000	Weak transcription	HepG2	liver
49	chr1:220400400-220423000	Weak transcription	Pancreas	Pancrea
50	chr1:220400600-220407600	Weak transcription	Adipose Nuclei	Adipose

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