Variant report

Variant	rs17083112
Chromosome Location	chr4:54453676-54453677
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:54439397..54441582-chr4:54451989..54453798,2	K562	blood:
2	chr4:54452448..54454872-chr4:54483525..54486127,2	K562	blood:
3	chr4:54450499..54453685-chr4:54466144..54467975,3	MCF-7	breast:
4	chr4:54451873..54454267-chr4:54454529..54458106,3	K562	blood:
5	chr4:54450850..54455147-chr4:54455906..54459442,4	K562	blood:

Variant related genes	Relation type
ENSG00000248494	Chromatin interaction
ENSG00000072201	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10517304	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10517305	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11936500	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11942048	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11945338	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12186283	0.94[YRI][hapmap]
rs2099452	0.94[CEU][hapmap];0.94[JPT][hapmap];0.83[YRI][hapmap];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7691817	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[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	nsv829936	chr4:54367783-54556123	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv437918	chr4:54451175-54483569	Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv879014	chr4:54451246-54461548	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17083112	LNX1	cis	lymphoblastoid	GTEx

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:54425200-54457400	Weak transcription	Right Atrium	heart
2	chr4:54431200-54456600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr4:54439000-54454800	Weak transcription	Left Ventricle	heart
4	chr4:54439200-54454600	Weak transcription	Aorta	Aorta
5	chr4:54443600-54457000	Weak transcription	Colonic Mucosa	Colon
6	chr4:54444000-54454600	Weak transcription	Placenta	Placenta
7	chr4:54447400-54454800	Weak transcription	Gastric	stomach
8	chr4:54448600-54454600	Weak transcription	Esophagus	oesophagus
9	chr4:54448600-54457400	Weak transcription	HMEC	breast
10	chr4:54449200-54453800	Weak transcription	Pancreas	Pancrea
11	chr4:54449800-54453800	Enhancers	NHDF-Ad	bronchial
12	chr4:54450000-54454600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr4:54450800-54457000	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr4:54452400-54455600	Enhancers	Fetal Intestine Small	intestine
15	chr4:54452600-54454600	Weak transcription	Fetal Muscle Leg	muscle
16	chr4:54452600-54456200	Enhancers	Fetal Intestine Large	intestine
17	chr4:54452600-54456400	Weak transcription	Fetal Lung	lung
18	chr4:54452600-54458600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr4:54452600-54459600	Enhancers	HepG2	liver
20	chr4:54452800-54454800	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr4:54452800-54457400	Weak transcription	NHEK	skin
22	chr4:54452800-54458400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr4:54452800-54459000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr4:54453000-54457000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr4:54453000-54457200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr4:54453000-54457400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr4:54453000-54458800	Weak transcription	Small Intestine	intestine
28	chr4:54453200-54455800	Enhancers	Liver	Liver
29	chr4:54453200-54459200	Weak transcription	Osteobl	bone
30	chr4:54453400-54454000	Active TSS	Rectal Mucosa Donor 29	rectum
31	chr4:54453600-54453800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
32	chr4:54453600-54454000	Enhancers	Duodenum Mucosa	Duodenum
33	chr4:54453600-54454200	Enhancers	Fetal Kidney	kidney
34	chr4:54453600-54454400	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr4:54453600-54454800	Weak transcription	Fetal Heart	heart

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