Variant report

Variant	rs13376679
Chromosome Location	chr1:47726087-47726088
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:47693951..47697518-chr1:47723725..47731232,8	K562	blood:
2	chr1:47642334..47646964-chr1:47725886..47730593,7	K562	blood:
3	chr1:47717233..47719376-chr1:47724988..47726635,2	K562	blood:

Variant related genes	Relation type
ENSG00000225506	Chromatin interaction
ENSG00000224805	Chromatin interaction
ENSG00000162367	Chromatin interaction

Extended variants
information (count: 100 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:98)

rs_ID	r²[population]
rs10157734	0.86[ASN][1000 genomes]
rs10218615	0.86[ASN][1000 genomes]
rs10789509	0.86[ASN][1000 genomes]
rs11211489	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11211490	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11211492	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11211495	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11211500	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11211505	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11211512	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11211516	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11211526	0.86[ASN][1000 genomes]
rs11211537	0.86[ASN][1000 genomes]
rs11576796	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11577236	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11577960	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11578360	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11579854	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11580114	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11580148	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11583162	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11584518	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11587014	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11587107	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11587272	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11588964	0.86[ASN][1000 genomes]
rs12117686	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12118205	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12118206	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12123269	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12123358	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12129259	0.86[ASN][1000 genomes]
rs12129594	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12131978	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12132521	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12132909	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12134888	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12135037	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12139700	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12140580	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12143808	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12144920	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12145103	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12145974	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12184262	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12184269	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12184297	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12406951	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12407463	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12409300	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12410850	1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12718447	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[YRI][hapmap];0.82[AFR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12729251	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12738065	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12749507	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12751618	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12756634	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12757893	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13374382	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17103095	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17103168	1.00[CEU][hapmap];0.93[YRI][hapmap];0.86[ASN][1000 genomes]
rs17370386	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[ASN][1000 genomes]
rs2097	0.86[ASN][1000 genomes]
rs2098	0.86[ASN][1000 genomes]
rs2405787	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2622903	0.96[CEU][hapmap]
rs2622914	0.96[CEU][hapmap]
rs2820986	0.96[CEU][hapmap]
rs2897238	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs33980430	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34192192	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34979288	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35234940	0.86[ASN][1000 genomes]
rs35601384	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35856603	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4375315	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4481897	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56804458	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58891696	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60352530	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6660651	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6665067	0.80[ASN][1000 genomes]
rs6670458	0.86[ASN][1000 genomes]
rs6688323	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6688804	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6698471	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6698717	1.00[CHB][hapmap];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs67221389	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs67295054	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs67905093	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71502303	0.86[ASN][1000 genomes]
rs72686209	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7354822	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7415976	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7514213	0.86[ASN][1000 genomes]
rs7534328	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7548099	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9725517	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]

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	nsv441692	chr1:47713661-47729088	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats	Chromatin interactive region	5 gene(s)	inside rSNPs	n/a
2	nsv822531	chr1:47713892-47730083	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Enhancers	Chromatin interactive region	5 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs13376679	MKNK1	cis	cerebellum	SCAN
rs13376679	CCDC24	cis	cerebellum	SCAN
rs13376679	CMPK1	cis	parietal	SCAN

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:47705200-47766400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr1:47705600-47766400	Weak transcription	Primary T cells from cord blood	blood
3	chr1:47709800-47745000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:47711000-47727800	Weak transcription	A549	lung
5	chr1:47712600-47735000	Weak transcription	NHDF-Ad	bronchial
6	chr1:47712600-47742600	Weak transcription	Fetal Lung	lung
7	chr1:47712800-47729600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr1:47712800-47745600	Weak transcription	Fetal Brain Female	brain
9	chr1:47713000-47736400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr1:47713200-47745800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr1:47713800-47745800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr1:47714200-47726600	Weak transcription	NHLF	lung
13	chr1:47714400-47726200	Weak transcription	Fetal Intestine Small	intestine
14	chr1:47714400-47779200	Weak transcription	Small Intestine	intestine
15	chr1:47714600-47745800	Weak transcription	Primary B cells from cord blood	blood
16	chr1:47714600-47778400	Weak transcription	Fetal Heart	heart
17	chr1:47714800-47732000	Weak transcription	Duodenum Mucosa	Duodenum
18	chr1:47714800-47741200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr1:47714800-47742800	Weak transcription	Fetal Kidney	kidney
20	chr1:47714800-47746000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr1:47715400-47730000	Strong transcription	HUES6 Cell Line	embryonic stem cell
22	chr1:47715400-47740000	Strong transcription	HUES64 Cell Line	embryonic stem cell
23	chr1:47715600-47749200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr1:47715800-47735400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr1:47716600-47739200	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr1:47716600-47772600	Strong transcription	Dnd41	blood
27	chr1:47716800-47739000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr1:47717000-47745800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr1:47717600-47727800	Weak transcription	NHEK	skin
30	chr1:47718200-47746000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr1:47718800-47730600	Strong transcription	HUES48 Cell Line	embryonic stem cell
32	chr1:47718800-47739800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
33	chr1:47719800-47745800	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr1:47720200-47730400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr1:47720400-47728200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr1:47720400-47730400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr1:47720400-47741400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr1:47720400-47757000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr1:47720600-47727000	Strong transcription	Primary neutrophils fromperipheralblood	blood
40	chr1:47720600-47728200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr1:47720600-47766400	Weak transcription	Brain Germinal Matrix	brain
42	chr1:47720800-47728600	Weak transcription	Placenta	Placenta
43	chr1:47721000-47726200	Strong transcription	HUVEC	blood vessel
44	chr1:47721000-47735400	Weak transcription	Fetal Muscle Leg	muscle
45	chr1:47721000-47749000	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr1:47721400-47729000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
47	chr1:47721600-47766800	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr1:47722400-47726400	Strong transcription	HSMM	muscle
49	chr1:47722600-47726200	Strong transcription	H1 Cell Line	embryonic stem cell
50	chr1:47722600-47728200	Strong transcription	Cortex derived primary cultured neurospheres	brain

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