Variant report

Variant	rs1284852
Chromosome Location	chr1:213073013-213073014
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C1orf227-2	chr1:213072869-213073048	NONHSAT009413

Extended variants
information (count: 27 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10864023	0.91[ASN][1000 genomes]
rs10864028	0.97[ASN][1000 genomes]
rs10864029	0.97[ASN][1000 genomes]
rs11120062	0.90[ASN][1000 genomes]
rs11582817	0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11586464	0.92[ASN][1000 genomes]
rs12036853	0.91[ASN][1000 genomes]
rs12136547	0.88[ASN][1000 genomes]
rs12404754	0.86[CHB][hapmap];0.91[CHD][hapmap];0.82[JPT][hapmap];0.91[ASN][1000 genomes]
rs12405293	0.91[ASN][1000 genomes]
rs12567976	0.91[ASN][1000 genomes]
rs12754609	0.91[ASN][1000 genomes]
rs12755947	0.91[ASN][1000 genomes]
rs1284854	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1284855	0.91[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1284856	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1587175	0.86[CHB][hapmap];0.82[JPT][hapmap];0.91[ASN][1000 genomes]
rs2359325	0.91[ASN][1000 genomes]
rs3207090	0.86[CHB][hapmap];0.91[CHD][hapmap];0.82[JPT][hapmap];0.91[ASN][1000 genomes]
rs4951471	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4951474	0.86[CHB][hapmap];0.83[JPT][hapmap]
rs6670064	0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6702876	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7541559	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[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	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
2	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
3	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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1284852	FLVCR	cis	multi-tissue	Pritchard
rs1284852	FLVCR1	cis	Whole Blood	GTEx
rs1284852	LQK1	Cis_1M	lymphoblastoid	RTeQTL
rs1284852	LOC642946	cis	multi-tissue	Pritchard

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:213037600-213073200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:213043200-213073400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr1:213047000-213073600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr1:213049800-213073200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr1:213049800-213073200	Weak transcription	Spleen	Spleen
6	chr1:213052800-213073400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr1:213053400-213073800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr1:213053800-213073200	Strong transcription	HUES48 Cell Line	embryonic stem cell
9	chr1:213053800-213073200	Strong transcription	HUES6 Cell Line	embryonic stem cell
10	chr1:213054400-213073200	Strong transcription	HUES64 Cell Line	embryonic stem cell
11	chr1:213055000-213073600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr1:213055200-213073200	Strong transcription	H1 Cell Line	embryonic stem cell
13	chr1:213056200-213074200	Strong transcription	Duodenum Mucosa	Duodenum
14	chr1:213056400-213073400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr1:213056600-213073600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr1:213057000-213073400	Strong transcription	Fetal Intestine Large	intestine
17	chr1:213057600-213075000	Weak transcription	Right Ventricle	heart
18	chr1:213058000-213073400	Strong transcription	A549	lung
19	chr1:213059400-213073600	Strong transcription	Primary T cells from cord blood	blood
20	chr1:213062400-213073400	Weak transcription	Psoas Muscle	Psoas
21	chr1:213062600-213075000	Weak transcription	Thymus	Thymus
22	chr1:213063600-213074800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr1:213063800-213073200	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr1:213064400-213073200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr1:213064400-213073200	Weak transcription	NHDF-Ad	bronchial
26	chr1:213065400-213073800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr1:213065800-213073200	Weak transcription	Brain Cingulate Gyrus	brain
28	chr1:213066400-213075400	Weak transcription	Rectal Smooth Muscle	rectum
29	chr1:213067400-213073200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
30	chr1:213067400-213074800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr1:213067600-213073200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr1:213067800-213073200	Strong transcription	Liver	Liver
33	chr1:213067800-213073400	Strong transcription	Duodenum Smooth Muscle	Duodenum
34	chr1:213067800-213073400	Strong transcription	Monocytes-CD14+_RO01746	blood
35	chr1:213067800-213073600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr1:213067800-213073600	Strong transcription	Dnd41	blood
37	chr1:213067800-213076000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr1:213068000-213073200	Strong transcription	Primary B cells from cord blood	blood
39	chr1:213068400-213073200	Strong transcription	Primary monocytes fromperipheralblood	blood
40	chr1:213068400-213073600	Strong transcription	HSMM	muscle
41	chr1:213068400-213074800	Weak transcription	Primary neutrophils fromperipheralblood	blood
42	chr1:213068600-213073200	Strong transcription	Fetal Lung	lung
43	chr1:213068800-213073200	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr1:213069000-213073200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr1:213069200-213073400	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr1:213069200-213074800	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr1:213069400-213074000	Weak transcription	Fetal Heart	heart
48	chr1:213069600-213073200	Weak transcription	Placenta	Placenta
49	chr1:213069800-213073600	Weak transcription	HUVEC	blood vessel
50	chr1:213069800-213074400	Weak transcription	HepG2	liver

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