Variant report

Variant	rs10517305
Chromosome Location	chr4:54456774-54456775
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:54449977..54452019-chr4:54455062..54457400,2	MCF-7	breast:
2	chr4:53577014..53579334-chr4:54455969..54458582,2	K562	blood:
3	chr4:54441539..54444052-chr4:54456319..54458612,3	MCF-7	breast:
4	chr4:54441243..54444280-chr4:54454649..54458129,3	MCF-7	breast:
5	chr4:54449770..54452528-chr4:54455369..54457530,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000264585	Chromatin interaction
ENSG00000173966	Chromatin interaction
ENSG00000226950	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:7)

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];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11936500	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];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11942048	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11945338	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]
rs17083112	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]
rs2099452	0.94[CEU][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7691817	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.98[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
rs10517305	LNX1	cis	lymphoblastoid	GTEx

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:54425200-54457400	Weak transcription	Right Atrium	heart
2	chr4:54443600-54457000	Weak transcription	Colonic Mucosa	Colon
3	chr4:54448600-54457400	Weak transcription	HMEC	breast
4	chr4:54450800-54457000	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr4:54452600-54458600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr4:54452600-54459600	Enhancers	HepG2	liver
7	chr4:54452800-54457400	Weak transcription	NHEK	skin
8	chr4:54452800-54458400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr4:54452800-54459000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr4:54453000-54457000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr4:54453000-54457200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr4:54453000-54457400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr4:54453000-54458800	Weak transcription	Small Intestine	intestine
14	chr4:54453200-54459200	Weak transcription	Osteobl	bone
15	chr4:54454200-54458400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr4:54454600-54457800	Active TSS	Esophagus	oesophagus
17	chr4:54454600-54459000	Enhancers	Fetal Muscle Leg	muscle
18	chr4:54454800-54459000	Weak transcription	Aorta	Aorta
19	chr4:54455000-54456800	Enhancers	K562	blood
20	chr4:54455200-54456800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr4:54455400-54457000	Weak transcription	Gastric	stomach
22	chr4:54455400-54457400	Weak transcription	Fetal Muscle Trunk	muscle
23	chr4:54455400-54457600	Weak transcription	Right Ventricle	heart
24	chr4:54455400-54458400	Weak transcription	Left Ventricle	heart
25	chr4:54455600-54457800	Active TSS	Breast Myoepithelial Primary Cells	Breast
26	chr4:54455600-54458000	Active TSS	Rectal Mucosa Donor 29	rectum
27	chr4:54455800-54458000	Active TSS	Fetal Kidney	kidney
28	chr4:54455800-54458200	Weak transcription	Fetal Heart	heart
29	chr4:54455800-54459000	Enhancers	Adipose Nuclei	Adipose
30	chr4:54456000-54457200	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr4:54456000-54457400	Active TSS	Fetal Stomach	stomach
32	chr4:54456000-54457800	Active TSS	Placenta	Placenta
33	chr4:54456000-54458200	Active TSS	Duodenum Mucosa	Duodenum
34	chr4:54456000-54458200	Active TSS	Pancreas	Pancrea
35	chr4:54456000-54460000	Active TSS	Pancreatic Islets	Pancreatic Islet
36	chr4:54456200-54456800	Enhancers	HUES6 Cell Line	embryonic stem cell
37	chr4:54456200-54457600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr4:54456200-54457600	Active TSS	Rectal Smooth Muscle	rectum
39	chr4:54456200-54458000	Active TSS	Fetal Intestine Large	intestine
40	chr4:54456200-54458200	Active TSS	Duodenum Smooth Muscle	Duodenum
41	chr4:54456200-54458600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr4:54456400-54456800	Enhancers	HUES48 Cell Line	embryonic stem cell
43	chr4:54456400-54456800	Enhancers	HUES64 Cell Line	embryonic stem cell
44	chr4:54456400-54458000	Active TSS	Rectal Mucosa Donor 31	rectum
45	chr4:54456400-54458200	Active TSS	Stomach Mucosa	stomach
46	chr4:54456600-54456800	Enhancers	iPS-20b Cell Line	embryonic stem cell
47	chr4:54456600-54456800	Active TSS	Liver	Liver
48	chr4:54456600-54456800	Flanking Active TSS	Fetal Intestine Small	intestine
49	chr4:54456600-54457000	Bivalent Enhancer	Fetal Lung	lung
50	chr4:54456600-54457200	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell

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