Variant report

Variant	rs6541127
Chromosome Location	chr1:220401009-220401010
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	chr1:220390706..220392701-chr1:220399648..220402266,2	K562	blood:
2	chr1:220395865..220398692-chr1:220400712..220402951,3	K562	blood:

Extended variants
information (count: 29 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10863537	0.83[CHB][hapmap];0.82[JPT][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes]
rs10863538	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11118507	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12026681	1.00[CEU][hapmap];0.87[JPT][hapmap];0.91[EUR][1000 genomes]
rs1397958	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1588578	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2221833	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2667967	0.88[EUR][1000 genomes]
rs2667968	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2667969	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2667970	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2789792	0.81[LWK][hapmap]
rs2808008	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[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];0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[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];0.92[MEX][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2808012	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2808013	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2808016	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[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];0.91[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[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];0.92[MEX][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2808026	0.81[LWK][hapmap]
rs2814492	0.96[ASN][1000 genomes]
rs2814494	0.83[ASN][1000 genomes]
rs2814495	0.94[ASN][1000 genomes]
rs4142940	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4511114	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6696985	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7535619	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.96[MEX][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[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	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
rs6541127	C1orf115	cis	lymphoblastoid	seeQTL
rs6541127	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	chr1:220384200-220402800	Weak transcription	NHLF	lung
8	chr1:220384200-220404400	Weak transcription	Ovary	ovary
9	chr1:220384200-220408800	Weak transcription	A549	lung
10	chr1:220384200-220420600	Weak transcription	Fetal Kidney	kidney
11	chr1:220384200-220423000	Weak transcription	Esophagus	oesophagus
12	chr1:220384200-220425800	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr1:220384400-220413400	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr1:220384800-220401800	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr1:220384800-220404400	Weak transcription	HSMMtube	muscle
16	chr1:220384800-220408000	Weak transcription	Hela-S3	cervix
17	chr1:220384800-220417000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr1:220385000-220403400	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr1:220385000-220403800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr1:220385000-220405000	Weak transcription	Placenta	Placenta
21	chr1:220385400-220409000	Weak transcription	NH-A	brain
22	chr1:220385400-220419400	Weak transcription	HUVEC	blood vessel
23	chr1:220385600-220408000	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr1:220386200-220404000	Weak transcription	NHEK	skin
25	chr1:220387600-220401600	Weak transcription	Liver	Liver
26	chr1:220393000-220401800	Weak transcription	K562	blood
27	chr1:220393000-220405400	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr1:220393000-220441000	Weak transcription	NHDF-Ad	bronchial
29	chr1:220393200-220403400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr1:220393200-220408800	Weak transcription	Brain Angular Gyrus	brain
31	chr1:220393200-220413400	Weak transcription	Fetal Heart	heart
32	chr1:220393400-220403800	Weak transcription	Fetal Lung	lung
33	chr1:220393400-220404000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr1:220393400-220405000	Weak transcription	Osteobl	bone
35	chr1:220393400-220411400	Weak transcription	Fetal Brain Female	brain
36	chr1:220393800-220425800	Weak transcription	Gastric	stomach
37	chr1:220394000-220422600	Weak transcription	Thymus	Thymus
38	chr1:220394400-220407800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr1:220396600-220404400	Weak transcription	Primary T helper cells PMA-I stimulated	--
40	chr1:220397200-220404400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr1:220397600-220401200	Enhancers	Colon Smooth Muscle	Colon
42	chr1:220398200-220406200	Strong transcription	Primary T cells from cord blood	blood
43	chr1:220398200-220406400	Strong transcription	Monocytes-CD14+_RO01746	blood
44	chr1:220398400-220420400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr1:220398600-220403200	Weak transcription	HUES64 Cell Line	embryonic stem cell
46	chr1:220398600-220406400	Weak transcription	Brain Germinal Matrix	brain
47	chr1:220398800-220402000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
48	chr1:220398800-220407000	Strong transcription	Primary monocytes fromperipheralblood	blood
49	chr1:220399000-220401400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr1:220399000-220403600	Weak transcription	GM12878-XiMat	blood

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