Variant report

Variant	rs10782553
Chromosome Location	chr1:86073859-86073860
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:86073392..86075755-chr1:86077364..86079429,2	MCF-7	breast:
2	chr1:86045532..86047930-chr1:86071624..86075132,3	MCF-7	breast:
3	chr1:86050411..86052188-chr1:86071339..86074227,2	MCF-7	breast:
4	chr1:86046246..86048052-chr1:86073407..86075472,2	K562	blood:
5	chr1:86073205..86075088-chr1:86076581..86078830,2	K562	blood:
6	chr1:86044508..86046493-chr1:86071384..86074227,2	K562	blood:
7	chr1:86044046..86050058-chr1:86065602..86074449,16	MCF-7	breast:

Variant related genes	Relation type
ENSG00000272691	Chromatin interaction
ENSG00000142871	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1047892	0.81[JPT][hapmap]
rs1047895	0.82[CEU][hapmap];0.83[JPT][hapmap]
rs10873709	0.99[ASN][1000 genomes]
rs10873710	0.83[CHB][hapmap];0.94[JPT][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1094359	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11161641	0.99[ASN][1000 genomes]
rs11161643	0.87[CEU][hapmap];0.83[JPT][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11161645	0.83[JPT][hapmap];0.90[ASN][1000 genomes]
rs11578464	0.87[CEU][hapmap];0.83[CHB][hapmap];0.94[JPT][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12128916	0.83[CEU][hapmap]
rs1764285	0.82[CEU][hapmap];0.82[JPT][hapmap];0.82[EUR][1000 genomes]
rs1764291	0.83[CEU][hapmap];0.81[EUR][1000 genomes]
rs1764292	0.83[CEU][hapmap];0.81[EUR][1000 genomes]
rs1764299	0.83[CEU][hapmap];0.81[EUR][1000 genomes]
rs1775988	0.82[CEU][hapmap];0.83[JPT][hapmap]
rs1775990	0.81[CEU][hapmap]
rs1928626	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2389970	0.83[JPT][hapmap];0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2785081	0.82[JPT][hapmap]
rs2995537	0.83[CEU][hapmap];0.82[EUR][1000 genomes]
rs34448540	0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs373787	0.83[CEU][hapmap]
rs3767162	0.83[EUR][1000 genomes]
rs414618	0.83[JPT][hapmap]
rs418979	0.83[CEU][hapmap]
rs4949915	0.84[CHB][hapmap];0.89[JPT][hapmap];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6689925	0.89[EUR][1000 genomes]
rs6699497	0.82[EUR][1000 genomes]
rs709801	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7532758	0.82[CEU][hapmap];0.83[JPT][hapmap]
rs821379	0.83[EUR][1000 genomes]
rs821381	0.83[EUR][1000 genomes]
rs821386	0.83[CEU][hapmap];0.83[JPT][hapmap];0.83[EUR][1000 genomes]
rs821389	0.82[CEU][hapmap];0.83[JPT][hapmap];0.83[EUR][1000 genomes]
rs821393	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs821394	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs821396	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs821401	0.83[EUR][1000 genomes]
rs843969	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs952837	0.83[CEU][hapmap];0.82[EUR][1000 genomes]
rs9700177	0.82[EUR][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	esv3391173	chr1:86005637-86337469	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10782553	ZNHIT6	cis	lung	GTEx
rs10782553	C1orf181	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:86048800-86081200	Weak transcription	Gastric	stomach
2	chr1:86066600-86077000	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr1:86068000-86074600	Enhancers	Fetal Intestine Small	intestine
4	chr1:86068400-86074800	Enhancers	Fetal Intestine Large	intestine
5	chr1:86070000-86076800	Weak transcription	Stomach Smooth Muscle	stomach
6	chr1:86070600-86076600	Weak transcription	Fetal Stomach	stomach
7	chr1:86071200-86076600	Weak transcription	Fetal Lung	lung
8	chr1:86071200-86076800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr1:86071400-86074200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr1:86071400-86074200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr1:86071400-86075000	Enhancers	HSMM	muscle
12	chr1:86071400-86075400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr1:86071600-86074400	Enhancers	iPS-20b Cell Line	embryonic stem cell
14	chr1:86071600-86074600	Enhancers	HUVEC	blood vessel
15	chr1:86071600-86076600	Enhancers	NHDF-Ad	bronchial
16	chr1:86071600-86078800	Enhancers	NHLF	lung
17	chr1:86071800-86074200	Enhancers	NHEK	skin
18	chr1:86071800-86074400	Enhancers	HMEC	breast
19	chr1:86071800-86074400	Enhancers	NH-A	brain
20	chr1:86071800-86074600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr1:86071800-86074600	Enhancers	HSMMtube	muscle
22	chr1:86071800-86076800	Enhancers	Muscle Satellite Cultured Cells	--
23	chr1:86072000-86074000	Enhancers	iPS-15b Cell Line	embryonic stem cell
24	chr1:86072000-86074200	Enhancers	H1 Cell Line	embryonic stem cell
25	chr1:86072000-86074200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr1:86072000-86074200	Enhancers	iPS-18 Cell Line	embryonic stem cell
27	chr1:86072000-86074200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr1:86072000-86074400	Enhancers	HUES48 Cell Line	embryonic stem cell
29	chr1:86072000-86074400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr1:86072000-86074600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr1:86072200-86074200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr1:86072200-86074200	Enhancers	HUES64 Cell Line	embryonic stem cell
33	chr1:86072200-86077600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr1:86072400-86074200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr1:86072400-86074600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr1:86072400-86076600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr1:86072400-86076600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr1:86072600-86074400	Enhancers	H9 Cell Line	embryonic stem cell
39	chr1:86072600-86074400	Enhancers	Placenta	Placenta
40	chr1:86073000-86074400	Enhancers	HUES6 Cell Line	embryonic stem cell
41	chr1:86073000-86078200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr1:86073200-86074000	Flanking Active TSS	A549	lung
43	chr1:86073200-86075200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr1:86073200-86076800	Weak transcription	Fetal Heart	heart
45	chr1:86073200-86077000	Weak transcription	Ovary	ovary
46	chr1:86073200-86078400	Weak transcription	Pancreas	Pancrea
47	chr1:86073200-86082200	Weak transcription	Aorta	Aorta
48	chr1:86073400-86074200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr1:86073400-86074200	Flanking Active TSS	Osteobl	bone
50	chr1:86073600-86074200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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