Variant report

Variant	rs4951474
Chromosome Location	chr1:213088787-213088788
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:213087453..213089849-chr1:213098017..213100027,2	K562	blood:
2	chr1:212963885..212966841-chr1:213087848..213090181,3	K562	blood:
3	chr1:213088698..213090352-chr1:213094141..213096256,2	K562	blood:
4	chr1:213088299..213089124-chr10:91087481..91088095,2	Hela-S3	cervix:
5	chr1:212838488..212839107-chr1:213088444..213089233,2	K562	blood:
6	chr1:212923025..212923977-chr1:213088635..213089225,2	K562	blood:
7	chr1:212987850..212988584-chr1:213088350..213088901,2	MCF-7	breast:
8	chr1:213088750..213091393-chr1:213108145..213110146,2	K562	blood:
9	chr1:212988120..212988960-chr1:213088354..213089047,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000237980	Chromatin interaction
ENSG00000203705	Chromatin interaction
ENSG00000119917	Chromatin interaction
ENSG00000117697	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 21 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10864028	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10864029	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11120067	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11576299	0.87[AFR][1000 genomes]
rs11576311	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11582817	1.00[CEU][hapmap];0.91[CHB][hapmap];0.83[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11586314	0.86[AMR][1000 genomes]
rs11586464	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12140722	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12140754	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12184323	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12404754	0.82[CEU][hapmap];0.82[CHB][hapmap]
rs1284863	0.89[ASN][1000 genomes]
rs1587175	0.80[CEU][hapmap]
rs2201601	0.80[EUR][1000 genomes]
rs3207090	0.82[CEU][hapmap];0.82[CHB][hapmap]
rs3816952	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3816953	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3816956	0.88[ASN][1000 genomes]
rs3816957	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4951655	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6656128	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6656232	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6666277	0.81[AMR][1000 genomes]
rs6670064	0.96[CEU][hapmap];0.91[CHB][hapmap];0.83[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6679848	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6679938	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6679951	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7523310	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7523329	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7533476	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7533575	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs870547	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs871767	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[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	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

mRNA abundance (count:21)

SNP	Gene	Cis/trans	Tissue	Source
rs4951474	FLVCR1-AS1	cis	Esophagus Muscularis	GTEx
rs4951474	FLVCR1-AS1	cis	Esophagus Mucosa	GTEx
rs4951474	FLVCR1-AS1	cis	Stomach	GTEx
rs4951474	NSL1	Cis_1M	lymphoblastoid	RTeQTL
rs4951474	FLVCR1-AS1	cis	Whole Blood	GTEx
rs4951474	FLVCR1-AS1	cis	Artery Tibial	GTEx
rs4951474	LQK1	cis	uninvolved skin	skin_eQTL
rs4951474	FLVCR1-AS1	cis	Adipose Subcutaneous	GTEx
rs4951474	FLVCR1-AS1	cis	lung	GTEx
rs4951474	LQK1	Cis_1M	lymphoblastoid	RTeQTL
rs4951474	FLVCR1-AS1	cis	Nerve Tibial	GTEx
rs4951474	FLVCR1	Cis_1M	lymphoblastoid	RTeQTL
rs4951474	LQK1	cis	lesional skin	skin_eQTL
rs4951474	FLVCR1-AS1	cis	Muscle Skeletal	GTEx
rs4951474	FLVCR1-AS1	cis	Artery Aorta	GTEx
rs4951474	FLVCR1-AS1	cis	Skin Sun Exposed Lower leg	GTEx
rs4951474	VASH2	Cis_1M	lymphoblastoid	RTeQTL
rs4951474	FLVCR1-AS1	cis	Thyroid	GTEx
rs4951474	FLVCR1-AS1	cis	Heart Left Ventricle	GTEx
rs4951474	LQK1	cis	normal skin	skin_eQTL
rs4951474	FLVCR1	cis	multi-tissue	Pritchard

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:213073800-213089000	Weak transcription	Pancreas	Pancrea
2	chr1:213079600-213090000	Weak transcription	Right Atrium	heart
3	chr1:213083200-213089000	Active TSS	H9 Cell Line	embryonic stem cell
4	chr1:213086800-213094400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr1:213087200-213089800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr1:213088000-213088800	Flanking Active TSS	H1 Cell Line	embryonic stem cell
7	chr1:213088000-213088800	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
8	chr1:213088000-213088800	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
9	chr1:213088000-213089000	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
10	chr1:213088000-213089200	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
11	chr1:213088000-213089200	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
12	chr1:213088000-213089400	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
13	chr1:213088000-213089800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
14	chr1:213088000-213090200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr1:213088000-213090400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
16	chr1:213088000-213090400	Enhancers	Fetal Brain Male	brain
17	chr1:213088000-213090600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr1:213088000-213090600	Enhancers	Cortex derived primary cultured neurospheres	brain
19	chr1:213088000-213090800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
20	chr1:213088200-213088800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr1:213088200-213088800	Enhancers	Fetal Brain Female	brain
22	chr1:213088200-213089000	Enhancers	Brain Germinal Matrix	brain
23	chr1:213088200-213089200	Enhancers	Fetal Muscle Leg	muscle
24	chr1:213088200-213089600	Enhancers	Duodenum Smooth Muscle	Duodenum
25	chr1:213088200-213089600	Enhancers	Fetal Heart	heart
26	chr1:213088200-213090200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr1:213088200-213090600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr1:213088200-213090600	Enhancers	Fetal Muscle Trunk	muscle
29	chr1:213088400-213088800	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr1:213088400-213088800	Enhancers	Brain Substantia Nigra	brain
31	chr1:213088400-213088800	Enhancers	Fetal Kidney	kidney
32	chr1:213088400-213089000	Enhancers	Fetal Stomach	stomach
33	chr1:213088400-213089600	Flanking Active TSS	A549	lung
34	chr1:213088400-213089800	Enhancers	Brain Hippocampus Middle	brain
35	chr1:213088400-213089800	Enhancers	HSMMtube	muscle
36	chr1:213088400-213090400	Enhancers	Fetal Lung	lung
37	chr1:213088400-213090600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr1:213088400-213090600	Enhancers	K562	blood
39	chr1:213088400-213090800	Enhancers	GM12878-XiMat	blood
40	chr1:213088600-213088800	Enhancers	Adipose Nuclei	Adipose
41	chr1:213088600-213088800	Enhancers	Brain Anterior Caudate	brain
42	chr1:213088600-213088800	Enhancers	Brain Inferior Temporal Lobe	brain
43	chr1:213088600-213088800	Bivalent Enhancer	Duodenum Mucosa	Duodenum
44	chr1:213088600-213089000	Enhancers	Primary hematopoietic stem cells short term culture	blood
45	chr1:213088600-213089200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr1:213088600-213089200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr1:213088600-213089200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr1:213088600-213089200	Flanking Active TSS	Hela-S3	cervix
49	chr1:213088600-213089200	Flanking Active TSS	HepG2	liver
50	chr1:213088600-213089600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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