Variant report

Variant	rs12404754
Chromosome Location	chr1:213064096-213064097
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:213064005..213065889-chr1:213067307..213069362,2	K562	blood:

Extended variants
information (count: 41 )
Associated
traits (count: 30 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1047881	0.90[GIH][hapmap]
rs10779588	0.88[GIH][hapmap]
rs10779595	0.81[AMR][1000 genomes]
rs10864022	0.81[AMR][1000 genomes]
rs10864023	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10864028	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10864029	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11120062	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11576299	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11582817	0.82[CEU][hapmap];0.91[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11586464	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12036853	0.96[ASN][1000 genomes]
rs12136547	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12405293	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12567976	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12754609	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12755947	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12756625	0.90[GIH][hapmap]
rs1284852	0.91[ASN][1000 genomes]
rs1284854	0.91[ASN][1000 genomes]
rs1284855	0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1284856	0.98[ASN][1000 genomes]
rs1587175	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2047287	0.85[AMR][1000 genomes]
rs2201601	0.80[EUR][1000 genomes]
rs2279692	0.86[GIH][hapmap]
rs2291773	0.90[GIH][hapmap]
rs2359325	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3207090	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4951471	0.91[ASN][1000 genomes]
rs4951474	0.82[CEU][hapmap];0.82[CHB][hapmap]
rs6670064	0.91[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6702876	0.96[ASN][1000 genomes]
rs7541559	0.97[ASN][1000 genomes]
rs963328	0.86[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011186	chr1:213005165-213069563	Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv1013705	chr1:213005344-213064209	Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv1008383	chr1:213025546-213114894	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv998261	chr1:213029814-213064209	Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv998979	chr1:213029814-213073013	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv1007129	chr1:213037244-213083261	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:30)

SNP	Gene	Cis/trans	Tissue	Source
rs12404754	LQK1	cis	cerebellum	SCAN
rs12404754	NCRNA00292	cis	lymphoblastoid	seeQTL
rs12404754	NSL1	Cis_1M	lymphoblastoid	RTeQTL
rs12404754	FLVCR1-AS1	cis	Artery Aorta	GTEx
rs12404754	LOC642946	cis	multi-tissue	Pritchard
rs12404754	NSL1	cis	lymphoblastoid	seeQTL
rs12404754	FLVCR1-AS1	cis	Artery Tibial	GTEx
rs12404754	FLVCR1	cis	multi-tissue	Pritchard
rs12404754	LQK1	cis	uninvolved skin	skin_eQTL
rs12404754	FLVCR1	cis	lymphoblastoid	seeQTL
rs12404754	C1orf227	cis	cerebellum	SCAN
rs12404754	FLVCR1-AS1	cis	Skin Sun Exposed Lower leg	GTEx
rs12404754	FLVCR1-AS1	cis	Heart Left Ventricle	GTEx
rs12404754	FLVCR1-AS1	cis	lung	GTEx
rs12404754	VASH2	cis	parietal	SCAN
rs12404754	FLVCR1-AS1	cis	Adipose Subcutaneous	GTEx
rs12404754	FLVCR1-AS1	cis	Whole Blood	GTEx
rs12404754	LQK1	Cis_1M	lymphoblastoid	RTeQTL
rs12404754	LQK1	cis	lesional skin	skin_eQTL
rs12404754	LQK1	cis	normal skin	skin_eQTL
rs12404754	C1orf48	cis	multi-tissue	Pritchard
rs12404754	FLVCR1	Cis_1M	lymphoblastoid	RTeQTL
rs12404754	FLVCR1-AS1	cis	Nerve Tibial	GTEx
rs12404754	C4BPA	cis	cerebellum	SCAN
rs12404754	FLVCR1-AS1	cis	Esophagus Mucosa	GTEx
rs12404754	FLVCR1-AS1	cis	Thyroid	GTEx
rs12404754	FLVCR1-AS1	cis	Esophagus Muscularis	GTEx
rs12404754	FLVCR1-AS1	cis	Muscle Skeletal	GTEx
rs12404754	VASH2	Cis_1M	lymphoblastoid	RTeQTL
rs12404754	LQK1	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:213032600-213073000	Weak transcription	Colonic Mucosa	Colon
2	chr1:213032600-213073000	Weak transcription	Esophagus	oesophagus
3	chr1:213034400-213068000	Weak transcription	Colon Smooth Muscle	Colon
4	chr1:213034600-213067800	Weak transcription	NHLF	lung
5	chr1:213034600-213070600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr1:213035800-213073000	Weak transcription	Small Intestine	intestine
7	chr1:213036000-213070800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr1:213037600-213073200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr1:213038400-213072000	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr1:213039600-213073000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr1:213040400-213073000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr1:213043200-213073400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr1:213045000-213070800	Weak transcription	Pancreas	Pancrea
14	chr1:213046600-213066400	Strong transcription	Primary monocytes fromperipheralblood	blood
15	chr1:213047000-213073600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr1:213049000-213073000	Weak transcription	HSMMtube	muscle
17	chr1:213049800-213072400	Weak transcription	Fetal Brain Male	brain
18	chr1:213049800-213073200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr1:213049800-213073200	Weak transcription	Spleen	Spleen
20	chr1:213050000-213065000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr1:213050800-213065800	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr1:213051200-213064400	Strong transcription	Hela-S3	cervix
23	chr1:213052200-213073000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr1:213052600-213066000	Strong transcription	HepG2	liver
25	chr1:213052800-213073400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr1:213053200-213066200	Strong transcription	Dnd41	blood
27	chr1:213053400-213073800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr1:213053600-213073000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
29	chr1:213053800-213073200	Strong transcription	HUES48 Cell Line	embryonic stem cell
30	chr1:213053800-213073200	Strong transcription	HUES6 Cell Line	embryonic stem cell
31	chr1:213054000-213071000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
32	chr1:213054200-213071400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
33	chr1:213054400-213073200	Strong transcription	HUES64 Cell Line	embryonic stem cell
34	chr1:213055000-213073600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr1:213055200-213065600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr1:213055200-213066400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr1:213055200-213073200	Strong transcription	H1 Cell Line	embryonic stem cell
38	chr1:213055800-213066600	Strong transcription	H9 Cell Line	embryonic stem cell
39	chr1:213056000-213071200	Strong transcription	Primary B cells from peripheral blood	blood
40	chr1:213056000-213072200	Strong transcription	ES-I3 Cell Line	embryonic stem cell
41	chr1:213056200-213066200	Strong transcription	Duodenum Smooth Muscle	Duodenum
42	chr1:213056200-213072000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr1:213056200-213074200	Strong transcription	Duodenum Mucosa	Duodenum
44	chr1:213056400-213066400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr1:213056400-213068000	Strong transcription	Fetal Muscle Trunk	muscle
46	chr1:213056400-213070000	Strong transcription	K562	blood
47	chr1:213056400-213073400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr1:213056600-213066200	Strong transcription	Adipose Nuclei	Adipose
49	chr1:213056600-213066200	Strong transcription	Liver	Liver
50	chr1:213056600-213066600	Strong transcription	Primary hematopoietic stem cells short term culture	blood

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