Variant report

Variant	rs164385
Chromosome Location	chr5:68430044-68430045
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CCDC125-2	chr5:68430029-68430429	XLOC_004863

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1086000	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1086001	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs163190	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs164565	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs164567	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs164568	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs164706	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2069433	0.93[JPT][hapmap]
rs2617403	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2637143	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs337254	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs338682	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs338683	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs338685	0.94[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs338686	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs350097	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs351426	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs367245	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs454528	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56152197	0.92[ASN][1000 genomes]
rs645089	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73119301	0.91[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	nsv1018151	chr5:68377118-68667581	Enhancers Active TSS Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv881765	chr5:68379836-68448694	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv881766	chr5:68401941-68448694	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1035004	chr5:68405526-68670101	Strong transcription Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
5	nsv329464	chr5:68430040-68430147	Strong transcription Weak transcription ZNF genes & repeats Enhancers	lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:68391400-68431200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr5:68400200-68431200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr5:68406200-68438400	Weak transcription	Aorta	Aorta
4	chr5:68406400-68431600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr5:68410400-68431800	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr5:68412400-68434600	Weak transcription	Psoas Muscle	Psoas
7	chr5:68415600-68431400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr5:68416400-68445000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr5:68418600-68431200	Weak transcription	Gastric	stomach
10	chr5:68419200-68431600	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr5:68419400-68430600	Weak transcription	HUVEC	blood vessel
12	chr5:68420600-68434800	Weak transcription	Fetal Brain Male	brain
13	chr5:68421000-68431200	Weak transcription	Brain Angular Gyrus	brain
14	chr5:68421200-68431600	Weak transcription	Spleen	Spleen
15	chr5:68421400-68433400	Weak transcription	Left Ventricle	heart
16	chr5:68421600-68447000	Weak transcription	Ovary	ovary
17	chr5:68421800-68431400	Weak transcription	Lung	lung
18	chr5:68423600-68432600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr5:68423800-68432200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr5:68424000-68430200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr5:68424000-68431000	Weak transcription	HMEC	breast
22	chr5:68424000-68431600	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr5:68424000-68432200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr5:68424000-68434000	Weak transcription	Brain Germinal Matrix	brain
25	chr5:68424400-68433200	Weak transcription	Right Ventricle	heart
26	chr5:68424600-68431400	Weak transcription	Brain Cingulate Gyrus	brain
27	chr5:68424800-68431400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr5:68425000-68431600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr5:68425000-68433200	Weak transcription	Thymus	Thymus
30	chr5:68425400-68431400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr5:68425400-68434400	Weak transcription	Duodenum Mucosa	Duodenum
32	chr5:68425600-68431200	Weak transcription	Fetal Lung	lung
33	chr5:68425600-68431200	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr5:68425600-68431400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr5:68425600-68431600	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr5:68425600-68432000	Weak transcription	Brain Substantia Nigra	brain
37	chr5:68425600-68432000	Weak transcription	K562	blood
38	chr5:68425600-68432000	Weak transcription	NHEK	skin
39	chr5:68425600-68432200	Weak transcription	Fetal Thymus	thymus
40	chr5:68425600-68433200	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr5:68425800-68430800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
42	chr5:68425800-68431200	Weak transcription	GM12878-XiMat	blood
43	chr5:68425800-68431800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr5:68425800-68432000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr5:68425800-68432000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr5:68425800-68432200	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr5:68425800-68432200	Weak transcription	Stomach Smooth Muscle	stomach
48	chr5:68426000-68431200	Weak transcription	HUES48 Cell Line	embryonic stem cell
49	chr5:68426400-68431200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr5:68426400-68431800	Weak transcription	HUES64 Cell Line	embryonic stem cell

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