Variant report

Variant	rs10068883
Chromosome Location	chr5:127331614-127331615
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:127330309..127331833-chr5:127336258..127338063,2	K562	blood:
2	chr3:122227988..122228941-chr5:127331066..127332034,2	MCF-7	breast:

Extended variants
information (count: 25 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10050374	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10057561	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10064559	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10213776	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10900794	0.87[CEU][hapmap]
rs11738398	0.94[CEU][hapmap];0.82[MEX][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes]
rs12517005	0.87[CEU][hapmap]
rs13160751	0.84[EUR][1000 genomes]
rs2011576	0.94[CEU][hapmap];0.84[EUR][1000 genomes]
rs2409037	0.87[CEU][hapmap]
rs4835937	0.80[AFR][1000 genomes]
rs4836344	1.00[ASN][1000 genomes]
rs4836346	0.84[EUR][1000 genomes]
rs4836348	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6595796	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.87[LWK][hapmap];0.82[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6871743	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6889756	0.94[CEU][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.93[TSI][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs758181	0.94[CEU][hapmap];1.00[CHB][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7706518	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7717741	0.94[CEU][hapmap];0.81[GIH][hapmap];0.82[MEX][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes]
rs7726011	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9327463	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv599665	chr5:127327649-127336709	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv511301	chr5:127327649-127337086	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	esv1813981	chr5:127327649-127437401	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs10068883	SLC12A2	cis	cerebellum	SCAN
rs10068883	HINT1	cis	cerebellum	SCAN
rs10068883	LOC644869	cis	multi-tissue	Pritchard
rs10068883	SLC27A6	cis	parietal	SCAN
rs10068883	CDC42SE2	cis	cerebellum	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:127290600-127332000	Weak transcription	Aorta	Aorta
2	chr5:127297600-127332000	Weak transcription	Primary B cells from cord blood	blood
3	chr5:127297800-127358400	Weak transcription	Primary hematopoietic stem cells	blood
4	chr5:127304000-127333400	Weak transcription	Primary T cells from cord blood	blood
5	chr5:127306600-127333200	Weak transcription	Psoas Muscle	Psoas
6	chr5:127323800-127338200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr5:127324000-127333200	Weak transcription	Left Ventricle	heart
8	chr5:127324000-127333200	Weak transcription	Pancreas	Pancrea
9	chr5:127324000-127350400	Weak transcription	HSMMtube	muscle
10	chr5:127324200-127332200	Weak transcription	Brain Hippocampus Middle	brain
11	chr5:127324200-127334800	Weak transcription	K562	blood
12	chr5:127324200-127342800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr5:127324400-127334400	Weak transcription	Gastric	stomach
14	chr5:127324400-127337400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr5:127324400-127337400	Weak transcription	HMEC	breast
16	chr5:127324400-127337600	Weak transcription	NHEK	skin
17	chr5:127324400-127354800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr5:127324400-127358400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr5:127326200-127334800	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr5:127326400-127359400	Weak transcription	GM12878-XiMat	blood
21	chr5:127327800-127359400	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr5:127328200-127379800	Weak transcription	Esophagus	oesophagus
23	chr5:127328400-127333000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr5:127329400-127351600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr5:127329600-127333200	Weak transcription	Small Intestine	intestine
26	chr5:127329800-127334800	Weak transcription	A549	lung
27	chr5:127330200-127337400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr5:127330400-127332000	Weak transcription	Stomach Mucosa	stomach
29	chr5:127330400-127337400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr5:127330800-127331800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
31	chr5:127330800-127333000	Enhancers	Colon Smooth Muscle	Colon
32	chr5:127331000-127331800	Enhancers	Cortex derived primary cultured neurospheres	brain
33	chr5:127331400-127331800	Weak transcription	Ovary	ovary
34	chr5:127331400-127332200	Enhancers	Right Atrium	heart
35	chr5:127331400-127332800	Enhancers	Stomach Smooth Muscle	stomach
36	chr5:127331400-127333000	Weak transcription	Brain Angular Gyrus	brain
37	chr5:127331400-127333000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr5:127331400-127333200	Weak transcription	Right Ventricle	heart
39	chr5:127331400-127333800	Enhancers	Rectal Smooth Muscle	rectum
40	chr5:127331600-127333200	Weak transcription	Fetal Muscle Leg	muscle
41	chr5:127331600-127334200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr5:127331600-127334400	Weak transcription	Primary B cells from peripheral blood	blood

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