Variant report

Variant	rs439378
Chromosome Location	chr1:57784989-57784990
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 122 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:119)

rs_ID	r²[population]
rs10047071	0.92[CHD][hapmap];0.86[JPT][hapmap]
rs10047073	0.92[CHD][hapmap];0.86[JPT][hapmap]
rs10493219	0.88[CHD][hapmap];0.86[JPT][hapmap]
rs10493225	1.00[JPT][hapmap]
rs1077424	0.89[CHD][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1077425	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10889034	1.00[JPT][hapmap]
rs10889035	0.92[CEU][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10889036	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10889037	0.96[CEU][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10889038	0.92[CHD][hapmap]
rs10889039	0.92[CHD][hapmap]
rs10889042	0.88[CHD][hapmap]
rs10889044	0.86[JPT][hapmap]
rs11207010	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs11207011	0.89[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11207012	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11207013	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11207014	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11207015	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11207016	0.92[CHD][hapmap]
rs11207017	0.80[EUR][1000 genomes]
rs11207026	0.88[CHD][hapmap]
rs1149630	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11585751	0.84[CHD][hapmap];0.86[JPT][hapmap]
rs12044912	1.00[JPT][hapmap]
rs12046102	1.00[JPT][hapmap]
rs12061812	1.00[JPT][hapmap]
rs12085326	0.90[ASN][1000 genomes]
rs12087888	0.89[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs12119147	0.88[CEU][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12119210	0.92[CHD][hapmap];0.83[EUR][1000 genomes]
rs12126723	0.83[EUR][1000 genomes]
rs12128305	0.82[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs12132685	1.00[JPT][hapmap]
rs12136107	0.86[JPT][hapmap]
rs12137169	0.88[CHD][hapmap];0.86[JPT][hapmap]
rs12139429	0.88[CHD][hapmap]
rs12142821	1.00[JPT][hapmap]
rs12240237	0.86[JPT][hapmap]
rs1240439	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1240442	0.86[JPT][hapmap]
rs12405761	0.86[JPT][hapmap]
rs12568449	1.00[JPT][hapmap]
rs12726704	1.00[JPT][hapmap]
rs12741210	0.85[CEU][hapmap];0.80[EUR][1000 genomes]
rs12752978	1.00[JPT][hapmap]
rs1334239	1.00[JPT][hapmap]
rs1334240	1.00[JPT][hapmap]
rs1424463	0.84[JPT][hapmap]
rs1424465	0.82[ASW][hapmap];0.85[CEU][hapmap];0.92[CHD][hapmap];0.89[GIH][hapmap];0.80[EUR][1000 genomes]
rs1424467	0.92[CHD][hapmap];0.85[JPT][hapmap]
rs1424470	0.83[EUR][1000 genomes]
rs1504594	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs166514	1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17115686	0.88[CHD][hapmap];0.86[JPT][hapmap]
rs17423255	0.92[CHD][hapmap]
rs17424216	0.88[CHD][hapmap];0.86[JPT][hapmap]
rs17425017	0.88[CHD][hapmap];0.86[JPT][hapmap]
rs17425189	1.00[JPT][hapmap]
rs17456661	0.80[CHD][hapmap];1.00[JPT][hapmap]
rs17459384	0.86[JPT][hapmap]
rs17459948	1.00[JPT][hapmap]
rs1809976	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1862925	0.85[CEU][hapmap];0.92[CHD][hapmap];0.89[GIH][hapmap];0.80[EUR][1000 genomes]
rs2113456	0.81[ASN][1000 genomes]
rs2161808	0.82[EUR][1000 genomes]
rs2216808	0.92[CHD][hapmap];0.86[JPT][hapmap]
rs2405696	0.86[JPT][hapmap]
rs2405697	0.82[ASW][hapmap];0.92[CHD][hapmap];0.80[GIH][hapmap]
rs2405994	0.84[CHD][hapmap];0.86[JPT][hapmap]
rs267638	1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs267646	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs267647	0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs267650	0.89[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs267651	0.84[CHD][hapmap]
rs269038	0.92[CHD][hapmap];0.80[GIH][hapmap]
rs269045	0.88[CHD][hapmap]
rs269049	0.88[CHD][hapmap]
rs2781325	1.00[JPT][hapmap]
rs28706213	0.83[ASN][1000 genomes]
rs35804651	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs374845	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3850549	0.88[CHD][hapmap]
rs3850552	0.84[CHD][hapmap]
rs3850556	0.80[CHD][hapmap]
rs3861834	0.84[CHD][hapmap]
rs3896279	0.88[CHD][hapmap]
rs390203	0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3909556	0.88[CHD][hapmap];0.86[JPT][hapmap]
rs4279875	1.00[JPT][hapmap]
rs4912163	1.00[JPT][hapmap]
rs4912244	0.86[JPT][hapmap]
rs532926	0.88[CHD][hapmap]
rs540431	0.88[CHD][hapmap]
rs563099	0.88[CHD][hapmap]
rs563270	0.86[CHD][hapmap]
rs566847	0.84[CHD][hapmap]
rs567773	0.92[CHD][hapmap]
rs61769668	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6587767	0.84[CHD][hapmap]
rs6669975	1.00[JPT][hapmap]
rs6677561	0.83[EUR][1000 genomes]
rs6687842	0.88[CHD][hapmap]
rs6687934	0.81[ASW][hapmap];0.85[CEU][hapmap];0.92[CHD][hapmap];0.89[GIH][hapmap];0.84[TSI][hapmap];0.81[EUR][1000 genomes]
rs736109	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs736110	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs746937	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7513076	0.86[JPT][hapmap]
rs7535763	0.92[CHD][hapmap];0.86[JPT][hapmap]
rs7543805	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7547509	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs77510	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs77511	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs882283	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs90940	0.96[CEU][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs924848	0.86[ASN][1000 genomes]
rs94216	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9436130	1.00[JPT][hapmap]

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	nsv461628	chr1:57463326-57816489	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv546305	chr1:57463326-57816489	Weak transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv871943	chr1:57784144-57855876	Weak transcription Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs439378	JUN	cis	cerebellum	SCAN
rs439378	DAB1	cis	cerebellum	SCAN
rs439378	C1orf168	cis	cerebellum	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:57773200-57790200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr1:57776600-57790200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr1:57780400-57787000	Weak transcription	Fetal Brain Male	brain
4	chr1:57784000-57785000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr1:57784000-57785400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr1:57784600-57785000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr1:57784600-57785200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr1:57784600-57785200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr1:57784600-57785200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
10	chr1:57784600-57785200	Enhancers	Fetal Muscle Leg	muscle
11	chr1:57784600-57785400	Enhancers	HUES6 Cell Line	embryonic stem cell
12	chr1:57784600-57785400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr1:57784600-57785400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr1:57784600-57785400	Enhancers	Fetal Brain Female	brain
15	chr1:57784600-57785600	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr1:57784600-57785600	Enhancers	Hela-S3	cervix
17	chr1:57784600-57785800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
18	chr1:57784600-57785800	Enhancers	Fetal Lung	lung
19	chr1:57784600-57786000	Enhancers	Duodenum Mucosa	Duodenum
20	chr1:57784800-57785200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr1:57784800-57785200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr1:57784800-57785200	Enhancers	HMEC	breast
23	chr1:57784800-57785400	Enhancers	NHEK	skin
24	chr1:57784800-57785600	Weak transcription	Brain Angular Gyrus	brain
25	chr1:57784800-57785600	Enhancers	Fetal Stomach	stomach
26	chr1:57784800-57786000	Enhancers	Fetal Intestine Large	intestine
27	chr1:57784800-57786000	Enhancers	Fetal Intestine Small	intestine

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