Variant report

Variant	rs1394629
Chromosome Location	chr5:118557513-118557514
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	chr5:118549930..118551447-chr5:118556250..118558321,2	K562	blood:

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10052879	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs10064311	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10071407	1.00[JPT][hapmap]
rs10900727	1.00[JPT][hapmap]
rs11241498	0.95[ASN][1000 genomes]
rs2036565	0.85[CEU][hapmap]
rs2404395	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2404396	0.90[AFR][1000 genomes]
rs2404398	0.89[AFR][1000 genomes]
rs3822516	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs4286709	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4380699	1.00[JPT][hapmap]
rs4533918	0.86[AFR][1000 genomes]
rs4583917	1.00[JPT][hapmap]
rs4895185	1.00[JPT][hapmap]
rs6595174	1.00[JPT][hapmap]
rs6595178	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6595179	0.89[ASN][1000 genomes]
rs6880622	1.00[JPT][hapmap]
rs6889308	1.00[JPT][hapmap]
rs7447270	0.92[EUR][1000 genomes]
rs7702867	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7720231	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7727906	0.85[CEU][hapmap]
rs7734532	1.00[JPT][hapmap];0.81[AFR][1000 genomes]
rs9327087	1.00[JPT][hapmap]
rs9327093	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv462426	chr5:118465249-118621672	Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv599564	chr5:118465249-118621672	ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv1016595	chr5:118468658-118621672	Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv1019788	chr5:118488501-118607405	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	nsv537882	chr5:118488501-118607405	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	nsv1034616	chr5:118506348-118600391	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
7	nsv1031914	chr5:118516878-118589497	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
8	esv2757136	chr5:118555863-118667748	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
9	esv2759374	chr5:118555863-118667748	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1394629	COL6A1	trans	lymphoblastoid	RTeQTL

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:118485800-118572200	Weak transcription	Small Intestine	intestine
2	chr5:118486000-118588600	Weak transcription	Right Ventricle	heart
3	chr5:118489800-118591200	Weak transcription	Colonic Mucosa	Colon
4	chr5:118498000-118584200	Weak transcription	Spleen	Spleen
5	chr5:118503800-118585800	Weak transcription	NH-A	brain
6	chr5:118507800-118580200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr5:118514400-118589000	Weak transcription	Pancreas	Pancrea
8	chr5:118514400-118591400	Weak transcription	Esophagus	oesophagus
9	chr5:118521200-118571000	Weak transcription	HMEC	breast
10	chr5:118524200-118570800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr5:118524400-118571000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr5:118524600-118561200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr5:118524600-118584200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr5:118534600-118574200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr5:118535000-118560800	Weak transcription	Gastric	stomach
16	chr5:118535000-118579600	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr5:118535000-118584800	Weak transcription	Brain Cingulate Gyrus	brain
18	chr5:118535000-118587400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr5:118535000-118588200	Weak transcription	Lung	lung
20	chr5:118535000-118589000	Weak transcription	Aorta	Aorta
21	chr5:118535200-118575200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr5:118535400-118569400	Weak transcription	Thymus	Thymus
23	chr5:118536400-118569800	Weak transcription	Brain Angular Gyrus	brain
24	chr5:118536400-118580000	Weak transcription	Fetal Brain Male	brain
25	chr5:118538200-118562000	Weak transcription	Brain Germinal Matrix	brain
26	chr5:118538200-118569000	Weak transcription	Ovary	ovary
27	chr5:118538200-118569400	Weak transcription	Fetal Brain Female	brain
28	chr5:118538200-118581800	Weak transcription	Brain Hippocampus Middle	brain
29	chr5:118538200-118586600	Weak transcription	Brain Substantia Nigra	brain
30	chr5:118538200-118590600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr5:118539200-118580800	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr5:118539200-118581600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr5:118539200-118590000	Weak transcription	Fetal Kidney	kidney
34	chr5:118539200-118591000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr5:118539400-118570600	Weak transcription	Primary T helper cells PMA-I stimulated	--
36	chr5:118540000-118569800	Weak transcription	Fetal Lung	lung
37	chr5:118540200-118557600	Weak transcription	Placenta	Placenta
38	chr5:118540200-118563200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr5:118540200-118569600	Weak transcription	Fetal Muscle Trunk	muscle
40	chr5:118540400-118558200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
41	chr5:118540600-118569000	Weak transcription	Fetal Muscle Leg	muscle
42	chr5:118540600-118569200	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr5:118540600-118569800	Weak transcription	Left Ventricle	heart
44	chr5:118540600-118569800	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr5:118540800-118558200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr5:118540800-118560800	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr5:118540800-118569600	Weak transcription	Primary neutrophils fromperipheralblood	blood
48	chr5:118544600-118591400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr5:118546200-118569600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr5:118547400-118573000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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