Variant report

Variant	rs2047293
Chromosome Location	chr1:213045521-213045522
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:213031111..213032891-chr1:213044814..213047099,3	MCF-7	breast:
2	chr1:213045207..213049301-chr1:213053372..213057994,4	K562	blood:
3	chr1:213036434..213038020-chr1:213044367..213045899,2	K562	blood:
4	chr1:213031272..213038020-chr1:213040720..213048331,10	K562	blood:
5	chr1:213039818..213042123-chr1:213045133..213047613,2	K562	blood:

Variant related genes	Relation type
ENSG00000198468	Chromatin interaction
ENSG00000162769	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10127459	1.00[ASN][1000 genomes]
rs10746436	1.00[ASN][1000 genomes]
rs10779594	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10864003	1.00[ASN][1000 genomes]
rs10864013	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10864017	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10864019	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11120033	1.00[ASN][1000 genomes]
rs12036735	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1284800	1.00[ASN][1000 genomes]
rs1284864	1.00[ASN][1000 genomes]
rs1615680	1.00[ASN][1000 genomes]
rs1692178	1.00[ASN][1000 genomes]
rs1692179	1.00[ASN][1000 genomes]
rs1692180	1.00[ASN][1000 genomes]
rs17020044	1.00[ASN][1000 genomes]
rs17020046	1.00[ASN][1000 genomes]
rs1770777	1.00[ASN][1000 genomes]
rs1770778	1.00[ASN][1000 genomes]
rs1874419	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2047289	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2047292	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2359324	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2456815	1.00[ASN][1000 genomes]
rs2644545	1.00[ASN][1000 genomes]
rs2792558	1.00[ASN][1000 genomes]
rs2792560	1.00[ASN][1000 genomes]
rs2792561	1.00[ASN][1000 genomes]
rs35976699	1.00[ASN][1000 genomes]
rs41315581	1.00[ASN][1000 genomes]
rs4418676	0.82[EUR][1000 genomes]
rs4951468	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4951649	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59252582	1.00[ASN][1000 genomes]
rs6540768	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6666362	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6667161	1.00[ASN][1000 genomes]
rs6674933	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6688865	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6689134	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6703612	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7528119	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7533932	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7542906	1.00[ASN][1000 genomes]
rs963327	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2047293	FLVCR1-AS1	cis	Artery Tibial	GTEx
rs2047293	FLVCR1-AS1	cis	Whole Blood	GTEx
rs2047293	FLVCR1-AS1	cis	Nerve Tibial	GTEx
rs2047293	LQK1	Cis_1M	lymphoblastoid	RTeQTL
rs2047293	FLVCR1	Cis_1M	lymphoblastoid	RTeQTL
rs2047293	FLVCR1-AS1	cis	Skin Sun Exposed Lower leg	GTEx
rs2047293	FLVCR1-AS1	cis	Heart Left Ventricle	GTEx
rs2047293	FLVCR1	cis	multi-tissue	Pritchard

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:213032600-213046400	Weak transcription	Ovary	ovary
2	chr1:213032600-213049200	Weak transcription	Right Atrium	heart
3	chr1:213032600-213073000	Weak transcription	Colonic Mucosa	Colon
4	chr1:213032600-213073000	Weak transcription	Esophagus	oesophagus
5	chr1:213032800-213046400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr1:213032800-213048000	Weak transcription	Rectal Smooth Muscle	rectum
7	chr1:213032800-213056800	Weak transcription	Fetal Thymus	thymus
8	chr1:213032800-213057800	Weak transcription	Placenta	Placenta
9	chr1:213032800-213061800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:213032800-213062000	Weak transcription	Psoas Muscle	Psoas
11	chr1:213033400-213046800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr1:213033400-213046800	Weak transcription	Stomach Smooth Muscle	stomach
13	chr1:213033600-213046800	Weak transcription	Liver	Liver
14	chr1:213033600-213048600	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr1:213033600-213062000	Weak transcription	Thymus	Thymus
16	chr1:213034400-213046200	Weak transcription	Fetal Lung	lung
17	chr1:213034400-213046600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr1:213034400-213046600	Weak transcription	Brain Cingulate Gyrus	brain
19	chr1:213034400-213048200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr1:213034400-213048400	Weak transcription	Brain Hippocampus Middle	brain
21	chr1:213034400-213058000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr1:213034400-213068000	Weak transcription	Colon Smooth Muscle	Colon
23	chr1:213034600-213046000	Weak transcription	HMEC	breast
24	chr1:213034600-213046400	Weak transcription	Brain Anterior Caudate	brain
25	chr1:213034600-213046400	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr1:213034600-213046600	Weak transcription	Primary B cells from peripheral blood	blood
27	chr1:213034600-213046800	Weak transcription	Primary B cells from cord blood	blood
28	chr1:213034600-213046800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr1:213034600-213046800	Weak transcription	NHDF-Ad	bronchial
30	chr1:213034600-213047400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr1:213034600-213048000	Weak transcription	Spleen	Spleen
32	chr1:213034600-213048600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr1:213034600-213048600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr1:213034600-213049200	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr1:213034600-213049200	Weak transcription	Lung	lung
36	chr1:213034600-213049400	Weak transcription	Gastric	stomach
37	chr1:213034600-213056200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr1:213034600-213057000	Weak transcription	Brain Substantia Nigra	brain
39	chr1:213034600-213057000	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr1:213034600-213057200	Weak transcription	Right Ventricle	heart
41	chr1:213034600-213061800	Weak transcription	Fetal Heart	heart
42	chr1:213034600-213067800	Weak transcription	NHLF	lung
43	chr1:213034600-213070600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr1:213035800-213046400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr1:213035800-213046400	Weak transcription	Brain Angular Gyrus	brain
46	chr1:213035800-213049400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr1:213035800-213073000	Weak transcription	Small Intestine	intestine
48	chr1:213036000-213070800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr1:213036200-213046800	Weak transcription	HUVEC	blood vessel
50	chr1:213036200-213062000	Weak transcription	Primary T killer memory cells from peripheral blood	blood

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