Variant report

Variant	rs2254158
Chromosome Location	chr1:225071943-225071944
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-WDR26-3	chr1:225071656-225071952	XLOC_001229

Extended variants
information (count: 81 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10158926	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1110378	0.85[AMR][1000 genomes]
rs1110379	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12563434	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1436176	0.82[JPT][hapmap]
rs1506069	0.94[CHB][hapmap];0.88[JPT][hapmap];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1506071	0.94[CHB][hapmap];0.97[CHD][hapmap];0.88[JPT][hapmap];0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1506072	0.82[JPT][hapmap]
rs1506074	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1936631	0.85[AMR][1000 genomes]
rs1936635	0.93[EUR][1000 genomes]
rs2014656	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2014667	0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2051158	0.92[ASN][1000 genomes]
rs2128268	0.94[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];0.88[JPT][hapmap];0.87[MKK][hapmap];0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2128270	0.82[JPT][hapmap]
rs2244102	0.91[ASN][1000 genomes]
rs2244126	0.91[ASN][1000 genomes]
rs2254406	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2406097	0.94[JPT][hapmap];0.84[AMR][1000 genomes]
rs2449256	0.94[CHB][hapmap];0.88[JPT][hapmap];0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2449258	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2449269	0.85[AMR][1000 genomes]
rs2449281	0.81[AMR][1000 genomes]
rs2449287	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2449304	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2449315	0.81[JPT][hapmap]
rs2449322	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2456336	0.94[CHB][hapmap];0.88[JPT][hapmap];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2456341	0.80[ASN][1000 genomes]
rs2456349	0.94[CHB][hapmap];0.88[JPT][hapmap];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2489296	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2489298	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2489301	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2489311	0.85[AMR][1000 genomes]
rs2489313	0.85[AMR][1000 genomes]
rs2489314	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2489324	0.82[JPT][hapmap]
rs2489327	0.94[CHB][hapmap];0.97[CHD][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs2489337	0.88[CHB][hapmap];0.94[CHD][hapmap];0.81[GIH][hapmap];0.88[JPT][hapmap];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2489343	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2489346	0.94[CHB][hapmap];0.88[JPT][hapmap];0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2489348	0.94[CHB][hapmap];0.97[CHD][hapmap];0.88[JPT][hapmap];0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2489352	0.94[CHB][hapmap];0.97[CHD][hapmap];0.88[JPT][hapmap];0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2489353	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2489355	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2501082	0.85[AMR][1000 genomes]
rs2501083	0.85[AMR][1000 genomes]
rs2501085	0.85[AMR][1000 genomes]
rs2501087	0.85[AMR][1000 genomes]
rs2501099	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2501100	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2501101	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2501107	0.87[CHB][hapmap]
rs2501108	0.87[CHB][hapmap];0.81[JPT][hapmap]
rs2501110	0.87[CHB][hapmap];0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2501133	0.85[ASN][1000 genomes]
rs2662917	0.82[JPT][hapmap]
rs2929626	0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2939363	0.94[CHB][hapmap];0.88[JPT][hapmap];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs3101904	0.81[AMR][1000 genomes]
rs3102106	0.87[ASN][1000 genomes]
rs3102115	0.81[AMR][1000 genomes]
rs3105558	0.87[CHB][hapmap]
rs3105564	0.81[AMR][1000 genomes]
rs3120989	0.81[AMR][1000 genomes]
rs3120991	0.80[AMR][1000 genomes]
rs3120993	0.81[AMR][1000 genomes]
rs3128654	0.81[AMR][1000 genomes]
rs3128655	0.81[AMR][1000 genomes]
rs3128657	0.83[AMR][1000 genomes]
rs3128664	0.80[AMR][1000 genomes]
rs57137890	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs59420435	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs61211002	0.81[AMR][1000 genomes]
rs61849768	0.84[ASN][1000 genomes]
rs6426163	1.00[CEU][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72629701	0.93[EUR][1000 genomes]
rs72629702	0.93[EUR][1000 genomes]
rs7530659	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs981067	0.87[CHB][hapmap]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2254158	NVL	cis	cerebellum	SCAN
rs2254158	TMEM63A	cis	cerebellum	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:225067000-225073000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr1:225068600-225072000	Weak transcription	Fetal Stomach	stomach
3	chr1:225069000-225072000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr1:225069000-225072400	Enhancers	iPS-20b Cell Line	embryonic stem cell
5	chr1:225069600-225073400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr1:225069600-225073400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr1:225069800-225072600	Weak transcription	A549	lung
8	chr1:225070200-225072800	Enhancers	Fetal Lung	lung
9	chr1:225070800-225072800	Enhancers	Fetal Intestine Large	intestine
10	chr1:225071000-225072800	Enhancers	Fetal Intestine Small	intestine
11	chr1:225071000-225072800	Enhancers	Fetal Kidney	kidney
12	chr1:225071200-225072600	Enhancers	Colon Smooth Muscle	Colon
13	chr1:225071200-225072800	Enhancers	HUES64 Cell Line	embryonic stem cell
14	chr1:225071400-225072200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
15	chr1:225071400-225072800	Enhancers	Rectal Mucosa Donor 29	rectum
16	chr1:225071600-225072600	Enhancers	HUES6 Cell Line	embryonic stem cell
17	chr1:225071600-225072600	Enhancers	iPS-15b Cell Line	embryonic stem cell
18	chr1:225071600-225072600	Enhancers	iPS-18 Cell Line	embryonic stem cell
19	chr1:225071600-225072800	Enhancers	H9 Cell Line	embryonic stem cell
20	chr1:225071600-225072800	Enhancers	Liver	Liver
21	chr1:225071600-225072800	Enhancers	Ovary	ovary
22	chr1:225071800-225072200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr1:225071800-225072400	Enhancers	Rectal Smooth Muscle	rectum
24	chr1:225071800-225072600	Enhancers	HUES48 Cell Line	embryonic stem cell
25	chr1:225071800-225073000	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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