Variant report

Variant	rs3768226
Chromosome Location	chr1:85808325-85808326
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	chr1:85808320..85810414-chr1:86046436..86048176,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000142871	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10493764	0.87[JPT][hapmap];0.86[ASN][1000 genomes]
rs11161618	1.00[YRI][hapmap]
rs11583836	1.00[YRI][hapmap]
rs12402128	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1523993	0.88[CHB][hapmap];0.89[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs17123650	1.00[YRI][hapmap]
rs17387935	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17590006	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35092233	0.88[ASN][1000 genomes]
rs35294786	0.86[ASN][1000 genomes]
rs35876501	0.86[ASN][1000 genomes]
rs35956189	0.83[ASN][1000 genomes]
rs36062892	0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs61769484	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61769490	0.90[ASN][1000 genomes]
rs61783046	0.86[ASN][1000 genomes]
rs6659486	0.86[ASN][1000 genomes]
rs6669293	0.98[ASN][1000 genomes]
rs6673833	1.00[CHB][hapmap];0.89[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs7540393	0.88[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]

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	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	esv34165	chr1:85542040-85846249	Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3768226	ZNHIT6	cis	cerebellum	SCAN
rs3768226	BCL10	cis	parietal	SCAN

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85796600-85809400	Weak transcription	Stomach Mucosa	stomach
2	chr1:85796800-85809600	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr1:85798800-85808400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr1:85798800-85808400	Weak transcription	Ovary	ovary
5	chr1:85798800-85824800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr1:85798800-85824800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr1:85799000-85813600	Weak transcription	Fetal Intestine Large	intestine
8	chr1:85800400-85808800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr1:85800400-85815000	Weak transcription	Fetal Intestine Small	intestine
10	chr1:85803600-85808600	Enhancers	HUVEC	blood vessel
11	chr1:85804200-85808600	Genic enhancers	HSMM	muscle
12	chr1:85804800-85811000	Enhancers	Muscle Satellite Cultured Cells	--
13	chr1:85805200-85809000	Weak transcription	Fetal Heart	heart
14	chr1:85805400-85808400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr1:85805600-85808400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr1:85805800-85811400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr1:85806000-85810400	Enhancers	Skeletal Muscle Female	skeletal muscle
18	chr1:85806400-85808600	Weak transcription	Fetal Kidney	kidney
19	chr1:85806400-85808800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr1:85806400-85815800	Weak transcription	Pancreas	Pancrea
21	chr1:85806600-85808400	Weak transcription	Colon Smooth Muscle	Colon
22	chr1:85806600-85813600	Weak transcription	Left Ventricle	heart
23	chr1:85806600-85814200	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr1:85806800-85808400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr1:85806800-85808400	Weak transcription	Adipose Nuclei	Adipose
26	chr1:85806800-85808400	Weak transcription	Psoas Muscle	Psoas
27	chr1:85806800-85809000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr1:85806800-85810200	Weak transcription	Lung	lung
29	chr1:85807000-85808800	Weak transcription	A549	lung
30	chr1:85807000-85809000	Weak transcription	HepG2	liver
31	chr1:85807200-85809000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr1:85807400-85809400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr1:85807400-85811000	Enhancers	NH-A	brain
34	chr1:85807600-85808600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr1:85807600-85808800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr1:85807600-85809200	Enhancers	HUES48 Cell Line	embryonic stem cell
37	chr1:85807600-85809600	Enhancers	ES-I3 Cell Line	embryonic stem cell
38	chr1:85807600-85810000	Enhancers	HSMMtube	muscle
39	chr1:85807600-85810200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr1:85807600-85810600	Enhancers	HUES64 Cell Line	embryonic stem cell
41	chr1:85807600-85810600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr1:85807600-85811000	Enhancers	iPS-20b Cell Line	embryonic stem cell
43	chr1:85807600-85811200	Enhancers	HUES6 Cell Line	embryonic stem cell
44	chr1:85807600-85812200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr1:85807600-85813400	Weak transcription	Fetal Muscle Trunk	muscle
46	chr1:85807800-85809600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr1:85807800-85810000	Enhancers	Skeletal Muscle Male	skeletal muscle
48	chr1:85807800-85810200	Enhancers	NHLF	lung
49	chr1:85807800-85810600	Enhancers	HMEC	breast
50	chr1:85807800-85811000	Enhancers	Cortex derived primary cultured neurospheres	brain

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