Variant report

Variant	rs2008798
Chromosome Location	chr19:42315406-42315407
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:42313500..42317243-chr19:42321753..42325232,3	K562	blood:
2	chr19:42314336..42316097-chr19:42330529..42333145,2	K562	blood:
3	chr19:42313100..42315480-chr19:42318084..42320585,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-DMRTC2-2	chr19:42315210-42315591	NR_102333

Extended variants
information (count: 84 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10401370	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10401528	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10401928	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10404939	0.90[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs10407206	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10407619	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10407797	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10408367	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10410918	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10414356	0.84[ASN][1000 genomes]
rs10414823	1.00[CEU][hapmap];0.95[CHB][hapmap];0.96[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10416824	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10417985	0.90[CHB][hapmap];0.83[JPT][hapmap]
rs10418100	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10419111	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10419827	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10426020	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10426049	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10426243	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10500284	0.92[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12976571	0.91[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs12979253	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12984383	0.90[CHB][hapmap];0.83[JPT][hapmap];0.80[YRI][hapmap]
rs1366610	0.90[CHB][hapmap];0.83[JPT][hapmap];0.89[YRI][hapmap]
rs1457144	0.90[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs1811564	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1870092	1.00[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap]
rs1870093	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2008808	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2075750	0.90[CHB][hapmap];0.83[JPT][hapmap];0.89[YRI][hapmap]
rs2075752	0.90[CHB][hapmap];0.83[JPT][hapmap]
rs2075754	0.90[CHB][hapmap];0.83[JPT][hapmap];0.89[YRI][hapmap]
rs2199829	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2199830	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2290695	0.90[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs2305809	0.90[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs28821622	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28824227	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28847113	0.90[EUR][1000 genomes]
rs34819714	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3786536	0.91[CHB][hapmap];0.83[JPT][hapmap]
rs3786538	0.90[CHB][hapmap];0.83[JPT][hapmap];0.94[YRI][hapmap]
rs3795022	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3810153	0.82[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap]
rs3922888	0.90[CHB][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs4130852	0.84[ASN][1000 genomes]
rs4480913	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4803511	0.90[CHB][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs4803512	0.85[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs62117403	0.90[EUR][1000 genomes]
rs6508998	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6508999	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6509000	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6509001	0.83[ASN][1000 genomes]
rs6509002	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs7248641	0.86[ASN][1000 genomes]
rs7251154	0.89[CEU][hapmap];0.83[EUR][1000 genomes]
rs7251336	1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7251783	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7251799	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7251960	1.00[CEU][hapmap];0.91[CHB][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7252877	0.81[ASN][1000 genomes]
rs7254214	0.90[CHB][hapmap];0.82[JPT][hapmap]
rs7258053	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7259967	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs734107	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs734109	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8099934	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8100182	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8104958	0.90[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs8106505	1.00[CEU][hapmap];0.95[CHB][hapmap];0.96[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8110199	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8113283	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8113538	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8113641	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8113720	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8113741	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8113780	0.86[ASN][1000 genomes]
rs8113813	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs873282	0.90[CHB][hapmap];0.83[JPT][hapmap];0.94[YRI][hapmap]
rs882520	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs891167	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs899662	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv522854	chr19:42120283-42931004	Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2008798	RABAC1	Cis_1M	lymphoblastoid	RTeQTL
rs2008798	DMRTC2	cis	Whole Blood	GTEx

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42304800-42316800	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr19:42310600-42317800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr19:42312000-42316600	Enhancers	Primary hematopoietic stem cells short term culture	blood
4	chr19:42312200-42316000	Enhancers	Primary hematopoietic stem cells	blood
5	chr19:42312200-42316400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
6	chr19:42313000-42316000	Enhancers	Primary B cells from peripheral blood	blood
7	chr19:42313000-42316400	Enhancers	Primary B cells from cord blood	blood
8	chr19:42313600-42316000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
9	chr19:42313800-42316200	Transcr. at gene 5' and 3'	Primary neutrophils fromperipheralblood	blood
10	chr19:42314200-42316000	Enhancers	Placenta	Placenta
11	chr19:42314400-42315600	Enhancers	GM12878-XiMat	blood
12	chr19:42314600-42315800	Weak transcription	Spleen	Spleen
13	chr19:42314600-42316000	Enhancers	Fetal Thymus	thymus
14	chr19:42314800-42315600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr19:42315400-42316200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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