Variant report

Variant	rs1379116
Chromosome Location	chr5:59942400-59942401
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 81 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10043291	0.87[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap]
rs10058456	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs10062240	0.88[CEU][hapmap]
rs10939855	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10939856	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10939860	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10939862	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11739724	0.86[ASN][1000 genomes]
rs11740327	0.81[CHB][hapmap];0.92[JPT][hapmap]
rs11741754	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs11948543	0.90[CHB][hapmap];0.92[JPT][hapmap];0.98[ASN][1000 genomes]
rs11951503	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11951950	0.88[ASN][1000 genomes]
rs11952735	0.98[ASN][1000 genomes]
rs11955398	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11956023	0.96[ASN][1000 genomes]
rs11959922	0.95[CHB][hapmap];0.92[JPT][hapmap];0.99[ASN][1000 genomes]
rs12514253	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12515025	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12517174	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.81[ASN][1000 genomes]
rs12517207	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs12522801	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1379114	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1379115	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1379117	1.00[ASN][1000 genomes]
rs1444237	0.88[CEU][hapmap];0.85[CHB][hapmap];0.93[JPT][hapmap]
rs1456742	1.00[CHB][hapmap];0.92[JPT][hapmap]
rs1456743	1.00[CHB][hapmap];0.92[JPT][hapmap]
rs1460958	0.83[CEU][hapmap];0.84[CHB][hapmap];0.92[JPT][hapmap]
rs153152	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1562235	0.90[ASN][1000 genomes]
rs17387940	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.82[ASN][1000 genomes]
rs1807017	0.84[CEU][hapmap]
rs1870014	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1992612	1.00[CHB][hapmap];0.92[JPT][hapmap]
rs2061250	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2198865	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2409792	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs248912	0.87[EUR][1000 genomes]
rs249070	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2591636	0.93[ASN][1000 genomes]
rs286153	0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs286154	0.81[CHB][hapmap];0.92[JPT][hapmap];0.83[ASN][1000 genomes]
rs286155	0.98[ASN][1000 genomes]
rs286156	0.91[ASN][1000 genomes]
rs286158	0.89[CHB][hapmap];0.84[JPT][hapmap];0.91[ASN][1000 genomes]
rs2898287	0.90[ASN][1000 genomes]
rs3857236	0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs3958943	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4277863	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs4504343	0.95[EUR][1000 genomes]
rs4524466	1.00[CHB][hapmap];0.92[JPT][hapmap]
rs4538566	0.95[EUR][1000 genomes]
rs4700378	0.82[ASN][1000 genomes]
rs4700379	0.84[ASN][1000 genomes]
rs4700380	0.96[ASN][1000 genomes]
rs4700381	0.89[ASN][1000 genomes]
rs5012862	0.84[ASN][1000 genomes]
rs55720622	0.88[ASN][1000 genomes]
rs55768631	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56137970	0.87[ASN][1000 genomes]
rs56166952	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56191602	0.99[ASN][1000 genomes]
rs56347749	0.95[EUR][1000 genomes]
rs59155887	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62372964	0.89[ASN][1000 genomes]
rs62373023	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62373024	0.81[ASN][1000 genomes]
rs6449493	1.00[CHB][hapmap];0.92[JPT][hapmap]
rs6874699	0.88[CEU][hapmap]
rs6877561	0.91[ASN][1000 genomes]
rs6896942	0.82[ASN][1000 genomes]
rs755077	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7704338	0.84[CEU][hapmap]
rs7719611	0.84[CEU][hapmap]
rs7719726	0.84[JPT][hapmap]
rs7720233	0.86[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap]
rs7730342	1.00[CHB][hapmap];0.92[JPT][hapmap]
rs9942410	1.00[CHB][hapmap];1.00[JPT][hapmap]

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	nsv598288	chr5:59627555-60003460	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
2	nsv492277	chr5:59905195-60180834	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1379116	ERCC8	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:59920600-59947800	Weak transcription	HUVEC	blood vessel
2	chr5:59925000-59942800	Strong transcription	Dnd41	blood
3	chr5:59925200-59947200	Weak transcription	Pancreas	Pancrea
4	chr5:59926400-59967800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr5:59926600-59946200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr5:59927200-59944000	Weak transcription	Fetal Muscle Leg	muscle
7	chr5:59928400-59942800	Weak transcription	Duodenum Mucosa	Duodenum
8	chr5:59929400-59942800	Weak transcription	Fetal Intestine Small	intestine
9	chr5:59929400-59944400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr5:59929400-59947400	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr5:59929400-59954600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr5:59929600-59948000	Weak transcription	NHEK	skin
13	chr5:59930000-59943400	Strong transcription	Placenta	Placenta
14	chr5:59931200-59942600	Strong transcription	HUES48 Cell Line	embryonic stem cell
15	chr5:59932000-59944200	Weak transcription	Primary hematopoietic stem cells	blood
16	chr5:59933200-59942400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr5:59933400-59965200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr5:59933600-59944000	Weak transcription	Fetal Stomach	stomach
19	chr5:59933600-59981000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr5:59933800-59942400	Strong transcription	HUES6 Cell Line	embryonic stem cell
21	chr5:59934000-59943000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr5:59934800-59947600	Weak transcription	HMEC	breast
23	chr5:59936600-59961400	Weak transcription	Thymus	Thymus
24	chr5:59936800-59961800	Weak transcription	Fetal Thymus	thymus
25	chr5:59937000-59943000	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr5:59937000-59945800	Weak transcription	GM12878-XiMat	blood
27	chr5:59937400-59943400	Strong transcription	HUES64 Cell Line	embryonic stem cell
28	chr5:59938000-59942600	Strong transcription	Monocytes-CD14+_RO01746	blood
29	chr5:59938600-59945200	Weak transcription	Fetal Kidney	kidney
30	chr5:59938800-59943000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr5:59939400-59942400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr5:59939800-59942800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr5:59940000-59943200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr5:59940400-59947800	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr5:59940400-59947800	Weak transcription	HSMM	muscle
36	chr5:59940600-59942400	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr5:59940600-59942400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr5:59940600-59943200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr5:59940600-59945000	Weak transcription	Fetal Intestine Large	intestine
40	chr5:59940600-59947400	Weak transcription	Primary neutrophils fromperipheralblood	blood
41	chr5:59940600-59947600	Weak transcription	A549	lung
42	chr5:59940600-59948000	Weak transcription	K562	blood
43	chr5:59940600-59950200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr5:59941000-59947200	Weak transcription	Primary monocytes fromperipheralblood	blood
45	chr5:59941200-59942400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr5:59941200-59946600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr5:59941200-59947600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr5:59941400-59942400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr5:59941400-59942400	Weak transcription	HepG2	liver
50	chr5:59942000-59942600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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