Variant report

Variant	rs578343
Chromosome Location	chr6:143069864-143069865
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:143069627..143071714-chr6:143222712..143224302,2	K562	blood:
2	chr6:143068612..143070141-chr6:143265805..143267834,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000010818	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs576420	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs580717	0.84[ASN][1000 genomes]
rs584733	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs597493	0.89[ASN][1000 genomes]
rs630537	1.00[CEU][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs638880	0.84[ASN][1000 genomes]
rs643298	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs654730	0.87[ASN][1000 genomes]
rs657775	0.89[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	nsv949088	chr6:142561402-143128849	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv830828	chr6:142970134-143116517	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
3	nsv830829	chr6:143058408-143218077	Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs578343	FBXO30	cis	parietal	SCAN
rs578343	HIVEP2	cis	parietal	SCAN
rs578343	HIVEP2	cis	cerebellum	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:143049800-143073200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr6:143054200-143072800	Weak transcription	Primary T cells from cord blood	blood
3	chr6:143059400-143072800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr6:143059400-143080600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr6:143059600-143074200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr6:143059800-143072400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr6:143062200-143074200	Weak transcription	NHEK	skin
8	chr6:143062400-143073600	Weak transcription	NHDF-Ad	bronchial
9	chr6:143062400-143074200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr6:143062600-143074200	Weak transcription	HSMM	muscle
11	chr6:143064000-143074000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr6:143066000-143073000	Weak transcription	HSMMtube	muscle
13	chr6:143066200-143074200	Weak transcription	HMEC	breast
14	chr6:143066200-143079000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr6:143066800-143074000	Weak transcription	Adipose Nuclei	Adipose
16	chr6:143066800-143074200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr6:143067600-143074200	Weak transcription	Brain Angular Gyrus	brain
18	chr6:143067600-143080600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr6:143067800-143074000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr6:143067800-143074200	Weak transcription	Aorta	Aorta
21	chr6:143067800-143074200	Weak transcription	Fetal Muscle Trunk	muscle
22	chr6:143068000-143072800	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr6:143068000-143074200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr6:143068000-143074200	Weak transcription	Brain Anterior Caudate	brain
25	chr6:143068000-143075000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr6:143068200-143073800	Weak transcription	Primary T helper cells fromperipheralblood	blood
27	chr6:143068200-143074200	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr6:143068200-143074200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr6:143068200-143074200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr6:143068200-143074200	Weak transcription	Thymus	Thymus
31	chr6:143068200-143077400	Weak transcription	Fetal Lung	lung
32	chr6:143068200-143079600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr6:143068400-143072800	Weak transcription	Fetal Thymus	thymus
34	chr6:143068400-143074000	Weak transcription	Primary T cells fromperipheralblood	blood
35	chr6:143069400-143072600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
36	chr6:143069600-143071800	Weak transcription	Fetal Brain Male	brain

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