Variant report

Variant	rs2568928
Chromosome Location	chr5:127487603-127487604
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	chr5:127486026..127488306-chr5:127501388..127503385,2	K562	blood:

Extended variants
information (count: 17 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1112956	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11948128	0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs17764730	1.00[ASW][hapmap];0.94[CEU][hapmap];0.85[CHB][hapmap];0.92[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.93[MKK][hapmap];0.90[TSI][hapmap];0.81[ASN][1000 genomes]
rs1993878	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2250127	0.94[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2409110	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2617617	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34576922	0.81[ASN][1000 genomes]
rs3749748	1.00[ASW][hapmap];0.94[CEU][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.93[MKK][hapmap];0.90[TSI][hapmap]
rs6860245	0.81[ASN][1000 genomes]
rs6888037	0.85[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs6889311	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7734927	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs790154	1.00[ASW][hapmap];0.94[CEU][hapmap];0.82[CHB][hapmap];0.82[CHD][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];0.88[MKK][hapmap];0.86[TSI][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs790155	1.00[ASW][hapmap];0.94[CEU][hapmap];0.82[CHB][hapmap];0.82[CHD][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];0.93[MKK][hapmap];0.87[TSI][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9327468	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[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	nsv830482	chr5:127475398-127665377	Strong transcription Genic enhancers Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2568928	CTC-228N24.3	cis	Muscle Skeletal	GTEx
rs2568928	CTC-228N24.3	cis	Skin Sun Exposed Lower leg	GTEx
rs2568928	CTC-228N24.3	cis	Thyroid	GTEx
rs2568928	FBN2	cis	cerebellum	SCAN
rs2568928	LOC644869	cis	multi-tissue	Pritchard

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:127423600-127494000	Weak transcription	K562	blood
2	chr5:127441200-127536800	Weak transcription	Colonic Mucosa	Colon
3	chr5:127442400-127525000	Weak transcription	Right Ventricle	heart
4	chr5:127445400-127491800	Weak transcription	Psoas Muscle	Psoas
5	chr5:127447000-127525000	Weak transcription	Fetal Brain Male	brain
6	chr5:127451400-127490600	Weak transcription	Aorta	Aorta
7	chr5:127451600-127488200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr5:127451800-127488600	Weak transcription	Osteobl	bone
9	chr5:127451800-127490400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr5:127452000-127490400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr5:127453600-127493800	Weak transcription	Liver	Liver
12	chr5:127453600-127525400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr5:127454400-127493800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr5:127457600-127534400	Weak transcription	Pancreas	Pancrea
15	chr5:127457800-127487800	Weak transcription	Stomach Mucosa	stomach
16	chr5:127457800-127489400	Weak transcription	NHEK	skin
17	chr5:127460800-127525200	Weak transcription	Spleen	Spleen
18	chr5:127461200-127488400	Weak transcription	HSMMtube	muscle
19	chr5:127463200-127533000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr5:127464200-127488400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr5:127464400-127489800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr5:127464800-127497600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr5:127465400-127532200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr5:127467000-127489000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr5:127467200-127500600	Weak transcription	Esophagus	oesophagus
26	chr5:127467600-127490200	Weak transcription	Lung	lung
27	chr5:127467600-127491200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr5:127467600-127525000	Weak transcription	Thymus	Thymus
29	chr5:127467800-127488800	Weak transcription	Fetal Intestine Small	intestine
30	chr5:127467800-127508000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr5:127468000-127489600	Weak transcription	Fetal Stomach	stomach
32	chr5:127468000-127536800	Weak transcription	Fetal Brain Female	brain
33	chr5:127468800-127493800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr5:127469200-127524200	Weak transcription	Monocytes-CD14+_RO01746	blood
35	chr5:127469800-127504200	Weak transcription	Fetal Heart	heart
36	chr5:127471200-127515200	Weak transcription	Brain Germinal Matrix	brain
37	chr5:127471800-127499800	Weak transcription	NHLF	lung
38	chr5:127472400-127498800	Weak transcription	Primary monocytes fromperipheralblood	blood
39	chr5:127473000-127488200	Weak transcription	HMEC	breast
40	chr5:127473400-127488400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr5:127473600-127521800	Weak transcription	Fetal Kidney	kidney
42	chr5:127474000-127489400	Weak transcription	Fetal Muscle Leg	muscle
43	chr5:127474000-127489800	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr5:127474200-127490000	Weak transcription	Rectal Smooth Muscle	rectum
45	chr5:127474400-127488200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr5:127474400-127488200	Weak transcription	Left Ventricle	heart
47	chr5:127474400-127491800	Weak transcription	Fetal Muscle Trunk	muscle
48	chr5:127474400-127493800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr5:127478000-127514400	Weak transcription	Primary neutrophils fromperipheralblood	blood
50	chr5:127478400-127489400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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