Variant report

Variant	rs2412488
Chromosome Location	chr4:54330867-54330868
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 82 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10000746	1.00[CEU][hapmap];0.88[CHB][hapmap];0.84[JPT][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10001201	0.86[CEU][hapmap];0.82[EUR][1000 genomes]
rs10005424	0.85[EUR][1000 genomes]
rs10007903	0.86[CEU][hapmap];0.86[EUR][1000 genomes]
rs10011259	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10017903	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10021541	0.81[EUR][1000 genomes]
rs10028142	0.88[EUR][1000 genomes]
rs1021099	0.81[EUR][1000 genomes]
rs11133266	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[YRI][hapmap];0.80[AFR][1000 genomes];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11722866	0.86[EUR][1000 genomes]
rs11723755	0.86[EUR][1000 genomes]
rs11725230	0.86[CEU][hapmap];0.86[EUR][1000 genomes]
rs11731499	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11734039	0.86[CEU][hapmap];0.81[EUR][1000 genomes]
rs11734681	0.82[CEU][hapmap];0.84[EUR][1000 genomes]
rs11947256	0.81[EUR][1000 genomes]
rs12507563	0.82[CEU][hapmap]
rs12507739	0.82[CEU][hapmap]
rs12508701	0.82[CEU][hapmap]
rs12511088	0.82[CEU][hapmap]
rs12511253	0.81[CEU][hapmap]
rs12642403	0.82[CEU][hapmap]
rs12649718	0.82[EUR][1000 genomes]
rs12651390	0.86[CEU][hapmap]
rs1471597	0.81[EUR][1000 genomes]
rs1481819	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1481824	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1531748	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1600795	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17082782	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17082893	0.82[CEU][hapmap]
rs17520800	0.88[EUR][1000 genomes]
rs2090117	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2271554	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2271559	0.81[CEU][hapmap]
rs2412447	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs28414913	0.88[EUR][1000 genomes]
rs28579268	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35499169	0.81[EUR][1000 genomes]
rs36011216	0.83[EUR][1000 genomes]
rs3765158	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3811782	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3811785	0.86[CEU][hapmap];0.87[EUR][1000 genomes]
rs4864759	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4864760	0.86[CEU][hapmap];0.81[EUR][1000 genomes]
rs4864767	0.82[CEU][hapmap]
rs56998298	0.81[EUR][1000 genomes]
rs6554100	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6554104	0.86[CEU][hapmap];0.81[EUR][1000 genomes]
rs6554105	0.86[CEU][hapmap];0.81[EUR][1000 genomes]
rs6554106	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6818788	0.82[CEU][hapmap]
rs6822201	0.82[CEU][hapmap]
rs6825364	0.86[EUR][1000 genomes]
rs6827269	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6828559	0.81[CEU][hapmap]
rs6833766	0.86[CEU][hapmap];0.86[EUR][1000 genomes]
rs6834934	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6838260	0.82[CEU][hapmap]
rs6839922	0.82[CEU][hapmap]
rs6840530	0.82[CEU][hapmap]
rs6848887	0.82[EUR][1000 genomes]
rs6852884	0.87[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6857024	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6857869	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6858320	0.86[AFR][1000 genomes]
rs7655975	0.81[EUR][1000 genomes]
rs7682199	0.85[EUR][1000 genomes]
rs7686876	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs7689981	0.85[EUR][1000 genomes]
rs7690908	0.88[EUR][1000 genomes]
rs7691578	0.86[EUR][1000 genomes]
rs7697622	0.82[EUR][1000 genomes]
rs7698792	0.86[CEU][hapmap];0.87[EUR][1000 genomes]
rs931181	0.86[CEU][hapmap];0.82[EUR][1000 genomes]
rs931182	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs967018	0.80[YRI][hapmap]
rs980987	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9995284	0.84[EUR][1000 genomes]
rs9996883	0.82[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3331791	chr4:54329721-54330939	Weak transcription Strong transcription	n/a	n/a	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
DNA methylation (variation)	23725790	GWAS catalog

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2412488	TYW1B	trans	parietal	SCAN
rs2412488	ZNF585A	cis	Frontal Cortex	GTEx
rs2412488	EXOC1	cis	cerebellum	SCAN
rs2412488	LYRM5	trans	cerebellum	SCAN

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:54292200-54331200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr4:54295200-54331600	Weak transcription	Hela-S3	cervix
3	chr4:54295600-54339400	Weak transcription	Fetal Brain Male	brain
4	chr4:54316800-54332600	Weak transcription	Esophagus	oesophagus
5	chr4:54317200-54331400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr4:54317400-54332600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr4:54320000-54332600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr4:54320000-54332600	Weak transcription	Aorta	Aorta
9	chr4:54320000-54332800	Weak transcription	Fetal Stomach	stomach
10	chr4:54320000-54342000	Weak transcription	Pancreas	Pancrea
11	chr4:54320000-54353200	Weak transcription	Gastric	stomach
12	chr4:54321000-54332600	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr4:54321200-54331800	Weak transcription	Ovary	ovary
14	chr4:54321400-54341800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr4:54321800-54339800	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr4:54322000-54331200	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr4:54322200-54331400	Weak transcription	Brain Anterior Caudate	brain
18	chr4:54322200-54331600	Weak transcription	HSMMtube	muscle
19	chr4:54322800-54331200	Weak transcription	Psoas Muscle	Psoas
20	chr4:54326400-54331200	Weak transcription	GM12878-XiMat	blood
21	chr4:54326400-54332200	Weak transcription	Fetal Intestine Small	intestine
22	chr4:54326400-54332600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr4:54327600-54347800	Weak transcription	Fetal Muscle Trunk	muscle
24	chr4:54327800-54331000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr4:54327800-54334600	Weak transcription	NHLF	lung
26	chr4:54327800-54335200	Weak transcription	HMEC	breast
27	chr4:54327800-54341800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr4:54327800-54362200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr4:54328000-54331200	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr4:54328000-54332000	Weak transcription	HUVEC	blood vessel
31	chr4:54328000-54332400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr4:54328000-54332600	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr4:54328000-54332800	Weak transcription	A549	lung
34	chr4:54328000-54339400	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr4:54328200-54332400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr4:54328200-54362000	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr4:54328400-54333600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr4:54328400-54362000	Weak transcription	Brain Angular Gyrus	brain
39	chr4:54328600-54331200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr4:54328600-54331800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr4:54328600-54332600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr4:54328600-54332600	Weak transcription	Fetal Muscle Leg	muscle
43	chr4:54328600-54339600	Weak transcription	Fetal Brain Female	brain
44	chr4:54329200-54331400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr4:54329200-54331400	Weak transcription	Primary T cells fromperipheralblood	blood
46	chr4:54329200-54332200	Weak transcription	Primary monocytes fromperipheralblood	blood
47	chr4:54329200-54332400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr4:54329200-54332400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr4:54329200-54332400	Weak transcription	Duodenum Mucosa	Duodenum
50	chr4:54329200-54332600	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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