Variant report

Variant	rs12408961
Chromosome Location	chr1:184049685-184049686
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1034477	0.94[ASN][1000 genomes]
rs10797941	0.94[ASN][1000 genomes]
rs11576332	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11582961	0.88[CEU][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11585756	0.94[ASN][1000 genomes]
rs12086203	0.88[ASN][1000 genomes]
rs12402790	0.85[CEU][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12403064	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12411231	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12725276	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12729638	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12734950	0.94[ASN][1000 genomes]
rs12751711	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12759837	0.89[ASN][1000 genomes]
rs1409812	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs16822379	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs17572231	1.00[CEU][hapmap]
rs1926873	0.94[ASN][1000 genomes]
rs1991170	0.94[ASN][1000 genomes]
rs34010717	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34876045	0.94[ASN][1000 genomes]
rs35178058	0.94[ASN][1000 genomes]
rs35514700	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35947721	0.94[ASN][1000 genomes]
rs4650654	0.94[ASN][1000 genomes]
rs56239295	0.94[ASN][1000 genomes]
rs58322431	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61477737	0.94[ASN][1000 genomes]
rs68130131	0.94[ASN][1000 genomes]
rs73053551	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs765224	0.88[CEU][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs765225	1.00[JPT][hapmap];0.94[ASN][1000 genomes]

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	nsv530079	chr1:183797938-184639971	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv533206	chr1:183861204-184091272	Enhancers Weak transcription Active TSS Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv1006655	chr1:183922288-184186677	Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12408961	C1orf19	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:184021600-184050400	Weak transcription	Gastric	stomach
2	chr1:184021600-184055800	Weak transcription	Esophagus	oesophagus
3	chr1:184022200-184053200	Weak transcription	Fetal Intestine Small	intestine
4	chr1:184023400-184052000	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr1:184024600-184063400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr1:184024600-184069400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr1:184024600-184079400	Weak transcription	Thymus	Thymus
8	chr1:184026600-184050400	Weak transcription	Aorta	Aorta
9	chr1:184026800-184052200	Weak transcription	HepG2	liver
10	chr1:184029800-184062000	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr1:184030800-184051600	Weak transcription	HSMMtube	muscle
12	chr1:184033600-184066600	Weak transcription	Pancreas	Pancrea
13	chr1:184035000-184066200	Weak transcription	Primary B cells from cord blood	blood
14	chr1:184035800-184073400	Weak transcription	Adipose Nuclei	Adipose
15	chr1:184036800-184064800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr1:184042400-184057600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr1:184042600-184054800	Weak transcription	NHEK	skin
18	chr1:184042600-184061800	Weak transcription	Psoas Muscle	Psoas
19	chr1:184043800-184071200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr1:184044000-184049800	Weak transcription	HSMM	muscle
21	chr1:184044000-184056600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr1:184044200-184063600	Weak transcription	Primary T cells from cord blood	blood
23	chr1:184044600-184052200	Weak transcription	Ovary	ovary
24	chr1:184044600-184062000	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr1:184046800-184057600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr1:184048200-184054000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr1:184048400-184051600	Weak transcription	Fetal Lung	lung
28	chr1:184048800-184051400	Weak transcription	Fetal Muscle Leg	muscle
29	chr1:184048800-184052200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr1:184048800-184061800	Weak transcription	Left Ventricle	heart
31	chr1:184048800-184063600	Weak transcription	Dnd41	blood
32	chr1:184049000-184051600	Weak transcription	Fetal Stomach	stomach

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