Variant report

Variant	rs6674620
Chromosome Location	chr1:169996593-169996594
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10800494	1.00[JPT][hapmap]
rs10800495	1.00[JPT][hapmap]
rs10919284	1.00[JPT][hapmap]
rs11585754	0.88[JPT][hapmap]
rs11803298	1.00[JPT][hapmap]
rs12123693	1.00[JPT][hapmap]
rs12124607	0.86[JPT][hapmap]
rs12126204	1.00[JPT][hapmap]
rs12137754	0.86[JPT][hapmap]
rs12144417	0.92[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12146137	1.00[JPT][hapmap]
rs12750962	1.00[JPT][hapmap]
rs13374766	0.88[JPT][hapmap]
rs1360293	1.00[JPT][hapmap]
rs2273457	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4656729	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4656737	0.88[JPT][hapmap]
rs6427233	1.00[JPT][hapmap]
rs6657512	1.00[JPT][hapmap]
rs6670191	1.00[JPT][hapmap]
rs688100	0.92[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7514634	0.85[JPT][hapmap]
rs7521273	0.85[JPT][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	nsv1014033	chr1:169968488-170453021	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
2	nsv535200	chr1:169968488-170453021	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6674620	SCYL3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169904000-170010400	Weak transcription	Aorta	Aorta
2	chr1:169951600-170011800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr1:169952000-170018000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr1:169952400-170043000	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr1:169956800-169997400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr1:169967600-170013000	Weak transcription	Fetal Heart	heart
7	chr1:169968800-169999400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr1:169968800-170010800	Weak transcription	Colon Smooth Muscle	Colon
9	chr1:169968800-170020200	Weak transcription	Brain Angular Gyrus	brain
10	chr1:169969000-169997400	Weak transcription	Fetal Stomach	stomach
11	chr1:169969000-170012600	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr1:169969600-170017800	Weak transcription	Esophagus	oesophagus
13	chr1:169979400-170018000	Weak transcription	Brain Cingulate Gyrus	brain
14	chr1:169979800-170015200	Weak transcription	HMEC	breast
15	chr1:169980000-170006600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr1:169980600-169997400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr1:169981600-170013400	Weak transcription	Lung	lung
18	chr1:169982400-170020600	Weak transcription	Rectal Smooth Muscle	rectum
19	chr1:169983000-170017200	Weak transcription	HSMMtube	muscle
20	chr1:169983800-170017600	Weak transcription	Spleen	Spleen
21	chr1:169984600-170020800	Weak transcription	Gastric	stomach
22	chr1:169984800-170027600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr1:169985000-169996600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr1:169985000-170010800	Weak transcription	Brain Hippocampus Middle	brain
25	chr1:169985000-170012800	Weak transcription	Brain Anterior Caudate	brain
26	chr1:169985200-169997000	Weak transcription	Primary B cells from cord blood	blood
27	chr1:169985200-170020400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr1:169985800-170003000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr1:169985800-170010800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr1:169985800-170010800	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr1:169986000-169996600	Weak transcription	Primary B cells from peripheral blood	blood
32	chr1:169986200-169996600	Weak transcription	Primary T cells from cord blood	blood
33	chr1:169986200-170006600	Weak transcription	Ovary	ovary
34	chr1:169986200-170010600	Weak transcription	Stomach Smooth Muscle	stomach
35	chr1:169986400-170013600	Weak transcription	Left Ventricle	heart
36	chr1:169986400-170019800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr1:169988000-170001200	Weak transcription	Osteobl	bone
38	chr1:169988000-170017600	Weak transcription	Fetal Lung	lung
39	chr1:169989200-170006400	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr1:169989600-170019800	Weak transcription	Right Ventricle	heart
41	chr1:169989800-170013400	Weak transcription	Psoas Muscle	Psoas
42	chr1:169990000-170004400	Weak transcription	Dnd41	blood
43	chr1:169990400-170017200	Weak transcription	Fetal Kidney	kidney
44	chr1:169991400-169997400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr1:169993000-169997400	Strong transcription	Primary T helper cells fromperipheralblood	blood
46	chr1:169993200-170002000	Weak transcription	Primary T cells fromperipheralblood	blood
47	chr1:169993600-170010800	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr1:169993600-170021400	Weak transcription	Fetal Brain Male	brain
49	chr1:169993800-170003000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr1:169994400-170001400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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