Variant report

Variant	rs1339768
Chromosome Location	chr1:180742308-180742309
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:180739733..180743864-chr1:180743918..180747985,4	K562	blood:

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10914096	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.91[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12085097	0.89[EUR][1000 genomes]
rs12118646	1.00[CHB][hapmap]
rs1970404	0.95[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2331626	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2331886	0.92[ASW][hapmap];1.00[CEU][hapmap];0.91[LWK][hapmap];0.89[TSI][hapmap];0.82[YRI][hapmap];0.86[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs2944259	0.84[CEU][hapmap];0.81[TSI][hapmap];0.90[EUR][1000 genomes]
rs2944262	0.89[CEU][hapmap];0.90[EUR][1000 genomes]
rs3002113	0.89[CEU][hapmap];0.90[EUR][1000 genomes]
rs3002114	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.91[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3002115	0.90[EUR][1000 genomes]
rs3002116	0.89[CEU][hapmap];0.81[TSI][hapmap];0.90[EUR][1000 genomes]
rs3002117	1.00[CEU][hapmap];0.95[CHB][hapmap];0.80[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3002123	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3013633	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3013634	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3789366	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3843278	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3845406	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap]
rs3856058	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.82[YRI][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3897798	0.86[ASN][1000 genomes]
rs4083591	1.00[ASW][hapmap];1.00[CEU][hapmap];0.96[MKK][hapmap];0.82[YRI][hapmap]
rs4108558	0.89[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs4651073	1.00[CHB][hapmap]
rs66520411	0.90[EUR][1000 genomes]
rs6659049	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6659368	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6661105	0.91[CHB][hapmap];0.86[CHD][hapmap]
rs6682974	0.89[CEU][hapmap];0.89[EUR][1000 genomes]
rs67780680	0.89[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs72707408	0.86[EUR][1000 genomes]
rs72723045	0.90[EUR][1000 genomes]
rs7514404	1.00[CEU][hapmap];0.87[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs7524547	0.90[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7541650	0.86[CHB][hapmap];0.84[CHD][hapmap];0.86[ASN][1000 genomes]
rs7548318	0.89[CEU][hapmap];0.81[TSI][hapmap];0.90[EUR][1000 genomes]
rs7550031	0.89[CEU][hapmap];0.89[EUR][1000 genomes]
rs9425881	0.94[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.91[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9970145	0.91[CHB][hapmap];0.81[CHD][hapmap]
rs9970363	0.91[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv872578	chr1:180510771-180842344	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv3777	chr1:180741213-180780313	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1339768	MR1	cis	parietal	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:180713000-180814200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr1:180715400-180747600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr1:180722600-180751000	Weak transcription	Left Ventricle	heart
4	chr1:180731800-180742400	Weak transcription	NHLF	lung
5	chr1:180738000-180751200	Weak transcription	Brain Anterior Caudate	brain
6	chr1:180740200-180751000	Weak transcription	Fetal Brain Female	brain
7	chr1:180740200-180753000	Weak transcription	Small Intestine	intestine
8	chr1:180740200-180761000	Weak transcription	Psoas Muscle	Psoas
9	chr1:180740800-180775600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr1:180741000-180757200	Weak transcription	Primary B cells from cord blood	blood
11	chr1:180741600-180784000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr1:180742000-180743400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr1:180742000-180743400	Enhancers	Muscle Satellite Cultured Cells	--
14	chr1:180742200-180742600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr1:180742200-180742600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
16	chr1:180742200-180742600	Enhancers	HSMMtube	muscle
17	chr1:180742200-180742800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr1:180742200-180743000	Enhancers	HMEC	breast
19	chr1:180742200-180743000	Enhancers	HUVEC	blood vessel
20	chr1:180742200-180743200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr1:180742200-180743200	Enhancers	NH-A	brain
22	chr1:180742200-180743200	Enhancers	NHDF-Ad	bronchial
23	chr1:180742200-180743400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr1:180742200-180743400	Genic enhancers	HSMM	muscle
25	chr1:180742200-180743400	Enhancers	Osteobl	bone

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