Variant report

Variant	rs6449527
Chromosome Location	chr5:60597127-60597128
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:60586340..60593423-chr5:60595007..60600646,11	MCF-7	breast:
2	chr5:60596613..60601643-chr5:60625817..60629986,6	MCF-7	breast:
3	chr5:60456737..60461436-chr5:60596585..60603587,8	MCF-7	breast:
4	chr5:60593618..60596553-chr5:60596973..60598822,2	K562	blood:
5	chr5:60595162..60604481-chr5:60621758..60631019,20	MCF-7	breast:
6	chr5:60457408..60460091-chr5:60596786..60599332,3	MCF-7	breast:
7	chr5:60595107..60599156-chr5:60625279..60628331,4	K562	blood:
8	chr5:60588266..60590443-chr5:60596275..60598423,2	MCF-7	breast:
9	chr5:60596572..60599250-chr5:60605731..60609279,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000188725	Chromatin interaction
ENSG00000130449	Chromatin interaction
ENSG00000251279	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10939897	0.84[CEU][hapmap]
rs10939900	0.81[CEU][hapmap];0.92[MEX][hapmap]
rs11747144	0.86[CEU][hapmap]
rs12520628	0.81[CEU][hapmap]
rs13154663	0.81[CEU][hapmap];0.87[CHD][hapmap]
rs13162866	0.87[CEU][hapmap]
rs13164720	0.87[CEU][hapmap]
rs13181015	0.81[CEU][hapmap];0.92[MEX][hapmap]
rs4132385	0.81[ASN][1000 genomes]
rs4235486	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4276369	0.81[CEU][hapmap]
rs4391122	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4421060	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4484384	0.81[CEU][hapmap]
rs4513641	0.87[CEU][hapmap];0.87[CHD][hapmap]
rs4544785	0.81[CEU][hapmap]
rs4546329	0.93[CHB][hapmap];0.82[CHD][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs4583848	0.95[ASN][1000 genomes]
rs6449525	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6449526	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.96[TSI][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6449530	0.81[CEU][hapmap];0.92[MEX][hapmap]
rs6860599	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6860608	0.81[CEU][hapmap];0.92[MEX][hapmap]
rs6867278	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6870349	0.81[CEU][hapmap];0.87[CHD][hapmap]
rs6877610	0.81[CEU][hapmap]
rs6889338	0.88[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[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	nsv1034038	chr5:60375328-60607654	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
2	nsv1028884	chr5:60414723-60732779	Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
3	nsv823089	chr5:60589501-60669903	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6449527	ERCC8	cis	cerebellum	SCAN

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:60587000-60597400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr5:60587200-60597200	Weak transcription	Brain Hippocampus Middle	brain
3	chr5:60587200-60597400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr5:60589200-60597200	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr5:60589400-60597400	Weak transcription	Brain Anterior Caudate	brain
6	chr5:60591800-60597400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr5:60593800-60597200	Enhancers	A549	lung
8	chr5:60594000-60602400	Enhancers	NHDF-Ad	bronchial
9	chr5:60594000-60602800	Enhancers	HMEC	breast
10	chr5:60594200-60597400	Enhancers	Fetal Lung	lung
11	chr5:60594400-60599200	Enhancers	Cortex derived primary cultured neurospheres	brain
12	chr5:60594600-60597200	Enhancers	Muscle Satellite Cultured Cells	--
13	chr5:60594600-60597200	Enhancers	Stomach Smooth Muscle	stomach
14	chr5:60594800-60597400	Weak transcription	Brain Cingulate Gyrus	brain
15	chr5:60594800-60597600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr5:60595000-60597600	Enhancers	iPS-15b Cell Line	embryonic stem cell
17	chr5:60595000-60599600	Weak transcription	Fetal Thymus	thymus
18	chr5:60595200-60597200	Weak transcription	Brain Substantia Nigra	brain
19	chr5:60595200-60597200	Weak transcription	Esophagus	oesophagus
20	chr5:60595200-60597200	Weak transcription	Left Ventricle	heart
21	chr5:60595200-60597200	Weak transcription	Right Atrium	heart
22	chr5:60595200-60597400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr5:60595200-60597400	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr5:60595200-60597400	Weak transcription	Lung	lung
25	chr5:60595200-60597400	Weak transcription	Psoas Muscle	Psoas
26	chr5:60595200-60597400	Weak transcription	Right Ventricle	heart
27	chr5:60595400-60597200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr5:60595400-60597200	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr5:60595400-60597200	Weak transcription	Stomach Mucosa	stomach
30	chr5:60595400-60597400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr5:60595400-60597400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr5:60595400-60597400	Weak transcription	Aorta	Aorta
33	chr5:60595400-60597800	Enhancers	NHEK	skin
34	chr5:60595400-60598800	Weak transcription	Ovary	ovary
35	chr5:60595600-60597200	Weak transcription	HUVEC	blood vessel
36	chr5:60595600-60597400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr5:60595800-60597200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr5:60595800-60597400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr5:60596000-60598400	Enhancers	HUES64 Cell Line	embryonic stem cell
40	chr5:60596200-60597200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr5:60596200-60597400	Weak transcription	Pancreas	Pancrea
42	chr5:60596400-60597200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr5:60596400-60597200	Enhancers	Osteobl	bone
44	chr5:60596400-60598000	Enhancers	HSMM	muscle
45	chr5:60596400-60598000	Enhancers	NH-A	brain
46	chr5:60596400-60598600	Enhancers	Brain Germinal Matrix	brain
47	chr5:60596600-60597400	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr5:60596800-60597200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr5:60596800-60597200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr5:60596800-60597400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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