Variant report

Variant	rs12042181
Chromosome Location	chr1:213088494-213088495
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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	chr1:213088299..213089124-chr10:91087481..91088095,2	Hela-S3	cervix:
4	chr1:212838488..212839107-chr1:213088444..213089233,2	K562	blood:
5	chr1:212987850..212988584-chr1:213088350..213088901,2	MCF-7	breast:
6	chr1:212988120..212988960-chr1:213088354..213089047,3	K562	blood:

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

Extended variants
information (count: 52 )
Associated
traits (count: 19 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1047881	0.87[CHB][hapmap];0.93[CHD][hapmap]
rs10779587	0.87[CHB][hapmap]
rs10779588	0.85[CHD][hapmap]
rs10779591	0.86[CHB][hapmap]
rs10864004	0.85[CHD][hapmap]
rs10864007	0.85[CHB][hapmap]
rs10864018	0.85[CHB][hapmap]
rs10864020	0.84[CHB][hapmap]
rs10902	0.91[CHB][hapmap];0.85[JPT][hapmap];0.86[YRI][hapmap]
rs11120043	0.86[CHD][hapmap]
rs11120047	0.86[CHB][hapmap]
rs11120057	0.85[CHB][hapmap]
rs11808574	0.86[CHB][hapmap]
rs12030572	0.94[CHB][hapmap];0.82[YRI][hapmap]
rs12048942	0.90[CHB][hapmap]
rs12567713	0.91[CHB][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];0.86[YRI][hapmap]
rs12567728	0.91[CHB][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];0.86[YRI][hapmap]
rs12756625	0.87[CHB][hapmap];0.95[CHD][hapmap]
rs1284860	0.87[CHB][hapmap]
rs17019818	0.91[CHB][hapmap];0.93[CHD][hapmap];0.86[YRI][hapmap]
rs17019870	0.91[CHB][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];0.82[YRI][hapmap]
rs1874420	0.85[CHB][hapmap];0.91[CHD][hapmap];0.85[YRI][hapmap]
rs1890932	0.91[CHB][hapmap];0.95[CHD][hapmap];0.86[YRI][hapmap]
rs2201602	0.86[CHB][hapmap]
rs2220949	0.87[CHB][hapmap]
rs2279692	0.85[CHD][hapmap]
rs2291772	0.91[CHB][hapmap];0.95[CHD][hapmap];0.86[YRI][hapmap]
rs2291773	0.87[CHB][hapmap];0.95[CHD][hapmap]
rs2497959	0.87[CHB][hapmap];0.93[CHD][hapmap]
rs2644548	0.87[CHB][hapmap];0.93[CHD][hapmap]
rs28529876	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3768548	0.91[CHB][hapmap];0.93[CHD][hapmap];0.86[YRI][hapmap]
rs3816954	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4951470	0.95[CHB][hapmap]
rs4951653	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs56129891	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6657416	0.87[CHB][hapmap]
rs6659996	0.86[CHB][hapmap]
rs6666277	0.87[CHB][hapmap];0.88[ASN][1000 genomes]
rs6666356	0.86[CHB][hapmap]
rs6666368	0.85[CHB][hapmap]
rs6700342	0.86[CHB][hapmap]
rs72743993	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7516718	0.87[CHB][hapmap]
rs7522693	0.87[CHB][hapmap]
rs7534973	0.87[CHB][hapmap];0.83[JPT][hapmap]
rs7536716	0.87[CHB][hapmap]
rs7544198	0.91[CHB][hapmap];0.93[CHD][hapmap];0.86[YRI][hapmap]
rs7544645	0.87[CHB][hapmap]
rs963328	0.85[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 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	esv3437401	chr1:213082329-213088502	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:19)

SNP	Gene	Cis/trans	Tissue	Source
rs12042181	FLVCR1-AS1	cis	lung	GTEx
rs12042181	BATF3	cis	lymphoblastoid	seeQTL
rs12042181	LQK1	Cis_1M	lymphoblastoid	RTeQTL
rs12042181	FLVCR1-AS1	cis	Skin Sun Exposed Lower leg	GTEx
rs12042181	FLVCR1-AS1	cis	Esophagus Muscularis	GTEx
rs12042181	FLVCR1-AS1	cis	Esophagus Mucosa	GTEx
rs12042181	FLVCR1-AS1	cis	Muscle Skeletal	GTEx
rs12042181	NCRNA00292	cis	lymphoblastoid	seeQTL
rs12042181	FLVCR1	cis	multi-tissue	Pritchard
rs12042181	LQK1	cis	parietal	SCAN
rs12042181	FLVCR1-AS1	cis	Heart Left Ventricle	GTEx
rs12042181	LQK1	cis	cerebellum	SCAN
rs12042181	FLVCR1-AS1	cis	Artery Aorta	GTEx
rs12042181	FLVCR1-AS1	cis	Whole Blood	GTEx
rs12042181	LOC642946	cis	multi-tissue	Pritchard
rs12042181	FLVCR1	Cis_1M	lymphoblastoid	RTeQTL
rs12042181	FLVCR	cis	multi-tissue	Pritchard
rs12042181	FLVCR1-AS1	cis	Adipose Subcutaneous	GTEx
rs12042181	FLVCR1-AS1	cis	Artery Tibial	GTEx

Chromatin state (count:47 , 50 per page) page: 1

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	chr1:213084200-213088600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr1:213086800-213094400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr1:213087200-213089800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr1:213087800-213088600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr1:213088000-213088600	Enhancers	Hela-S3	cervix
9	chr1:213088000-213088800	Flanking Active TSS	H1 Cell Line	embryonic stem cell
10	chr1:213088000-213088800	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
11	chr1:213088000-213088800	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
12	chr1:213088000-213089000	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
13	chr1:213088000-213089200	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
14	chr1:213088000-213089200	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
15	chr1:213088000-213089400	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
16	chr1:213088000-213089800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
17	chr1:213088000-213090200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr1:213088000-213090400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
19	chr1:213088000-213090400	Enhancers	Fetal Brain Male	brain
20	chr1:213088000-213090600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr1:213088000-213090600	Enhancers	Cortex derived primary cultured neurospheres	brain
22	chr1:213088000-213090800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
23	chr1:213088200-213088600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr1:213088200-213088600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr1:213088200-213088600	Enhancers	HepG2	liver
26	chr1:213088200-213088800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr1:213088200-213088800	Enhancers	Fetal Brain Female	brain
28	chr1:213088200-213089000	Enhancers	Brain Germinal Matrix	brain
29	chr1:213088200-213089200	Enhancers	Fetal Muscle Leg	muscle
30	chr1:213088200-213089600	Enhancers	Duodenum Smooth Muscle	Duodenum
31	chr1:213088200-213089600	Enhancers	Fetal Heart	heart
32	chr1:213088200-213090200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr1:213088200-213090600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr1:213088200-213090600	Enhancers	Fetal Muscle Trunk	muscle
35	chr1:213088400-213088600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
36	chr1:213088400-213088600	Enhancers	Fetal Thymus	thymus
37	chr1:213088400-213088800	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr1:213088400-213088800	Enhancers	Brain Substantia Nigra	brain
39	chr1:213088400-213088800	Enhancers	Fetal Kidney	kidney
40	chr1:213088400-213089000	Enhancers	Fetal Stomach	stomach
41	chr1:213088400-213089600	Flanking Active TSS	A549	lung
42	chr1:213088400-213089800	Enhancers	Brain Hippocampus Middle	brain
43	chr1:213088400-213089800	Enhancers	HSMMtube	muscle
44	chr1:213088400-213090400	Enhancers	Fetal Lung	lung
45	chr1:213088400-213090600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr1:213088400-213090600	Enhancers	K562	blood
47	chr1:213088400-213090800	Enhancers	GM12878-XiMat	blood

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