Variant report

Variant	rs17123306
Chromosome Location	chr1:62734089-62734090
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11803521	1.00[CEU][hapmap];0.81[CHB][hapmap];0.82[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17123303	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17123307	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17123318	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17123328	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17123329	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3850630	0.86[CHB][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55812433	1.00[ASN][1000 genomes]
rs59318560	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59838506	0.97[ASN][1000 genomes]
rs61623093	0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1004446	chr1:62394631-62813533	Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
2	nsv534984	chr1:62394631-62813533	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
3	nsv1009398	chr1:62656660-62780644	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1013582	chr1:62723703-62910632	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	31 gene(s)	inside rSNPs	diseases
5	esv3408127	chr1:62729964-62734262	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17123306	D4S234E	trans	lymphoblastoid	seeQTL
rs17123306	L1TD1	cis	lymphoblastoid	seeQTL

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:62711600-62737200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:62721000-62739400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
3	chr1:62728000-62734800	Weak transcription	Fetal Brain Male	brain
4	chr1:62729000-62737600	Weak transcription	Right Atrium	heart
5	chr1:62729400-62734400	Strong transcription	Placenta Amnion	Placenta Amnion
6	chr1:62729600-62736800	Weak transcription	Fetal Muscle Leg	muscle
7	chr1:62729600-62737400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr1:62729600-62737400	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr1:62729600-62737600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr1:62729600-62737800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr1:62729800-62737400	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr1:62731400-62734600	Strong transcription	Fetal Muscle Trunk	muscle
13	chr1:62731400-62734800	Strong transcription	HepG2	liver
14	chr1:62732000-62734800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
15	chr1:62732000-62734800	Weak transcription	Rectal Smooth Muscle	rectum
16	chr1:62732200-62737000	Weak transcription	Esophagus	oesophagus
17	chr1:62732200-62737600	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr1:62732400-62734200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr1:62732400-62737000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr1:62732400-62737400	Weak transcription	Fetal Kidney	kidney
21	chr1:62732400-62737600	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr1:62732400-62737600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr1:62732400-62737600	Weak transcription	Placenta	Placenta
24	chr1:62732400-62740000	Weak transcription	Liver	Liver
25	chr1:62732400-62748400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr1:62732800-62737600	Weak transcription	Fetal Intestine Small	intestine
27	chr1:62733000-62741000	Weak transcription	Brain Germinal Matrix	brain
28	chr1:62733200-62734800	Enhancers	Pancreas	Pancrea
29	chr1:62733200-62737400	Weak transcription	Fetal Lung	lung
30	chr1:62733800-62734200	Enhancers	Gastric	stomach
31	chr1:62734000-62735000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr1:62734000-62735000	Strong transcription	Fetal Stomach	stomach
33	chr1:62734000-62737400	Weak transcription	Adipose Nuclei	Adipose

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