Variant report

Variant	rs1329961
Chromosome Location	chr1:86050700-86050701
allele	C/T
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	chr1:85957596..85960543-chr1:86049198..86051756,2	K562	blood:
2	chr1:86045233..86051336-chr1:86057804..86069814,19	K562	blood:
3	chr1:86043660..86051626-chr1:86167839..86177430,17	K562	blood:
4	chr1:85931646..85934591-chr1:86050681..86053602,2	MCF-7	breast:
5	chr1:86049707..86051912-chr1:86063181..86065060,2	MCF-7	breast:
6	chr1:86049608..86052158-chr1:86093207..86095698,2	MCF-7	breast:
7	chr1:86050411..86052188-chr1:86071339..86074227,2	MCF-7	breast:
8	chr1:86046116..86050935-chr1:86168336..86177340,12	K562	blood:
9	chr1:86048276..86051402-chr1:86117655..86121071,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000117174	Chromatin interaction
ENSG00000230285	Chromatin interaction
ENSG00000273264	Chromatin interaction
ENSG00000199934	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs12061951	0.81[CEU][hapmap]
rs12072027	0.92[ASW][hapmap];0.95[CEU][hapmap];0.82[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12239954	0.86[CEU][hapmap];0.82[CHB][hapmap];0.89[JPT][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1576423	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6658857	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6673340	0.84[EUR][1000 genomes]
rs9651137	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9803850	0.85[ASW][hapmap];0.91[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.91[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1329961	ZNHIT6	cis	lymphoblastoid	seeQTL

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:86048400-86052000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr1:86048600-86053400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr1:86048800-86050800	Enhancers	HepG2	liver
4	chr1:86048800-86051000	Weak transcription	Brain Anterior Caudate	brain
5	chr1:86048800-86053600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr1:86048800-86081200	Weak transcription	Gastric	stomach
7	chr1:86049000-86050800	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr1:86049000-86051000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr1:86049000-86052200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr1:86049000-86052200	Weak transcription	Pancreas	Pancrea
11	chr1:86049000-86053600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr1:86049000-86053600	Weak transcription	Fetal Intestine Small	intestine
13	chr1:86049000-86068400	Weak transcription	Psoas Muscle	Psoas
14	chr1:86049200-86050800	Weak transcription	Liver	Liver
15	chr1:86049200-86050800	Active TSS	HSMM	muscle
16	chr1:86049200-86051000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr1:86049200-86051000	Active TSS	HUVEC	blood vessel
18	chr1:86049200-86051600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr1:86049200-86053200	Weak transcription	Left Ventricle	heart
20	chr1:86049200-86053600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr1:86049400-86050800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr1:86049400-86051000	Enhancers	NHEK	skin
23	chr1:86049400-86053200	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr1:86049400-86053600	Weak transcription	Fetal Muscle Trunk	muscle
25	chr1:86049400-86053600	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr1:86049600-86051000	Active TSS	NHDF-Ad	bronchial
27	chr1:86049600-86051600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr1:86049800-86050800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr1:86049800-86050800	Enhancers	Fetal Stomach	stomach
30	chr1:86049800-86050800	Active TSS	NHLF	lung
31	chr1:86049800-86051000	Enhancers	iPS-15b Cell Line	embryonic stem cell
32	chr1:86049800-86051000	Active TSS	Breast Myoepithelial Primary Cells	Breast
33	chr1:86049800-86051000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr1:86049800-86051000	Enhancers	Fetal Lung	lung
35	chr1:86049800-86051200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr1:86050000-86050800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr1:86050000-86050800	Enhancers	Fetal Kidney	kidney
38	chr1:86050000-86050800	Flanking Active TSS	A549	lung
39	chr1:86050000-86051000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr1:86050000-86051000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr1:86050000-86051000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr1:86050000-86051800	Enhancers	HUES48 Cell Line	embryonic stem cell
43	chr1:86050000-86051800	Enhancers	HMEC	breast
44	chr1:86050200-86050800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
45	chr1:86050200-86051200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
46	chr1:86050200-86052000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr1:86050200-86052000	Enhancers	Fetal Heart	heart
48	chr1:86050200-86053400	Weak transcription	Stomach Smooth Muscle	stomach
49	chr1:86050200-86053600	Weak transcription	Adipose Nuclei	Adipose
50	chr1:86050200-86053600	Weak transcription	Fetal Muscle Leg	muscle

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