Variant report

Variant	rs10494266
Chromosome Location	chr1:150245552-150245553
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:61)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAZ	chr1:150244580-150245977	IMR90	lung:	n/a	n/a
2	POLR2A	chr1:150244413-150245927	H1-hESC	embryonic stem cell:	n/a	n/a
3	MTA3	chr1:150245541-150246134	GM12878	blood:	n/a	n/a
4	MYC	chr1:150245414-150245567	NB4	blood:	n/a	n/a
5	CTCF	chr1:150245420-150245570	AG09309	skin:	n/a	n/a
6	CTCF	chr1:150245480-150245630	HPAF	blood vessel:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:150245537-150245587	GM12892	blood:	n/a
2	chr1:150245537-150245587	HCM	heart:	n/a
3	chr1:150245537-150245587	HL-60	blood:	n/a
4	chr1:150245537-150245587	HRPEpiC	eye:	n/a
5	chr1:150245537-150245587	AG04450	lung:	fetal
6	chr1:150245537-150245587	HCF	heart:	n/a
7	chr1:150245537-150245587	GM12878	blood:	n/a
8	chr1:150245537-150245587	HUVEC	blood vessel:	n/a
9	chr1:150245537-150245587	Caco-2	colon:	n/a
10	chr1:150245537-150245587	MCF10A-Er-Src	breast:	n/a
11	chr1:150245537-150245587	CMK	blood:	n/a
12	chr1:150245537-150245587	HPAEpiC	pulmonary alveolar:	n/a
13	chr1:150245537-150245587	AoSMC	blood vessel:	n/a
14	chr1:150245537-150245587	HMEC	breast:	n/a
15	chr1:150245537-150245587	HCPEpiC	choroid plexus:	n/a
16	chr1:150245537-150245587	HepG2	liver:	n/a
17	chr1:150245537-150245587	AG04449	skin:	fetal
18	chr1:150245537-150245587	HNPCEpiC	eye:	n/a
19	chr1:150245537-150245587	MCF-7	breast:	n/a
20	chr1:150245537-150245587	SK-N-MC	brain:	n/a
21	chr1:150245537-150245587	GM06990	blood:	n/a
22	chr1:150245537-150245587	Hela-S3	cervix:	n/a
23	chr1:150245537-150245587	ECC-1	luminal epithelium:	n/a
24	chr1:150245537-150245587	Hepatocyte	liver:	n/a
25	chr1:150245537-150245587	K562	blood:	n/a
26	chr1:150245537-150245587	GM19239	blood:	n/a
27	chr1:150245537-150245587	HIPEpiC	eye:	n/a
28	chr1:150245537-150245587	LNCaP	prostate:	n/a
29	chr1:150245537-150245587	ProgFib	skin:	n/a
30	chr1:150245537-150245587	IMR90	lung:	fetal
31	chr1:150245537-150245587	PrEC	prostate:	n/a
32	chr1:150245537-150245587	SAEC	small airway:	n/a
33	chr1:150245537-150245587	HRCEpiC	kidney:	n/a
34	chr1:150245537-150245587	AG10803	skin:	n/a
35	chr1:150245537-150245587	BJ	skin:	n/a
36	chr1:150245537-150245587	T-47D	breast:	n/a
37	chr1:150245537-150245587	NB4	blood:	n/a
38	chr1:150245537-150245587	NHBE	bronchial:	n/a
39	chr1:150245537-150245587	Jurkat	blood:	n/a
40	chr1:150245537-150245587	HEEpiC	esophagus:	n/a
41	chr1:150245537-150245587	NH-A	brain:	n/a
42	chr1:150245537-150245587	H1-hESC	embryonic stem cell:	embryo
43	chr1:150245537-150245587	HAEpiC	amniotic membrane:	n/a
44	chr1:150245537-150245587	U87	brain:	n/a
45	chr1:150245537-150245587	SK-N-SH_RA	brain:	n/a
46	chr1:150245537-150245587	AG09309	skin:	n/a
47	chr1:150245537-150245587	RPTEC	kidney:	n/a
48	chr1:150245537-150245587	PANC-1	pancreas:	n/a
49	chr1:150245537-150245587	NT2-D1	testis:	n/a
50	chr1:150245537-150245587	HRE	kidney:	n/a

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:150228680..150231125-chr1:150243640..150246471,2	K562	blood:
2	chr1:150245244..150248880-chr1:150251272..150253316,4	K562	blood:

No data

Variant related genes	Relation type
APH1A	TF binding region
APH1A	CpG island
ENSG00000118298	Chromatin interaction
ENSG00000271845	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs11205363	0.81[CEU][hapmap]
rs12027008	0.81[CEU][hapmap];0.88[GIH][hapmap];0.95[TSI][hapmap]
rs12129776	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2275780	0.89[CEU][hapmap];0.82[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[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	nsv529719	chr1:150006344-150311095	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	100 gene(s)	inside rSNPs	diseases
2	nsv916014	chr1:150187139-150537483	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	164 gene(s)	inside rSNPs	diseases
3	nsv872415	chr1:150210538-150248046	Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv1009508	chr1:150211112-150270830	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
5	nsv535154	chr1:150214907-150265508	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
6	nsv1011223	chr1:150229205-150279380	Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10494266	MRPS21	cis	cerebellum	SCAN
rs10494266	TMOD4	cis	cerebellum	SCAN
rs10494266	MRPS21	cis	parietal	SCAN
rs10494266	CTSS	cis	cerebellum	SCAN

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:150241800-150253400	Weak transcription	Ovary	ovary
2	chr1:150241800-150253800	Weak transcription	Esophagus	oesophagus
3	chr1:150241800-150253800	Weak transcription	Gastric	stomach
4	chr1:150241800-150254200	Weak transcription	Spleen	Spleen
5	chr1:150242000-150253400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr1:150242000-150253800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr1:150242200-150246000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr1:150242200-150248200	Weak transcription	Duodenum Mucosa	Duodenum
9	chr1:150242200-150248600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr1:150242200-150250000	Weak transcription	Liver	Liver
11	chr1:150242200-150252600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr1:150242200-150253200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr1:150242200-150253200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr1:150242200-150253400	Weak transcription	Primary T cells from cord blood	blood
15	chr1:150242200-150253400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr1:150242400-150248200	Weak transcription	Primary T helper cells fromperipheralblood	blood
17	chr1:150242400-150253000	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr1:150242400-150253200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr1:150242600-150253200	Weak transcription	Primary T helper cells PMA-I stimulated	--
20	chr1:150243800-150245800	Enhancers	K562	blood
21	chr1:150244000-150246800	Enhancers	Primary monocytes fromperipheralblood	blood
22	chr1:150244600-150245600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
23	chr1:150244600-150245600	Enhancers	Muscle Satellite Cultured Cells	--
24	chr1:150244600-150245800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr1:150244600-150245800	Active TSS	Fetal Muscle Trunk	muscle
26	chr1:150244600-150245800	Flanking Active TSS	Stomach Smooth Muscle	stomach
27	chr1:150244600-150246000	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
28	chr1:150244600-150246000	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
29	chr1:150244600-150246000	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
30	chr1:150244600-150246000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
31	chr1:150244600-150246000	Flanking Active TSS	Adipose Nuclei	Adipose
32	chr1:150244600-150246000	Flanking Active TSS	Fetal Muscle Leg	muscle
33	chr1:150244600-150246200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr1:150244600-150246400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr1:150244600-150246400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr1:150244600-150246600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr1:150244600-150246600	Flanking Active TSS	Osteobl	bone
38	chr1:150244800-150245600	Enhancers	Primary hematopoietic stem cells short term culture	blood
39	chr1:150244800-150245600	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr1:150244800-150245600	Active TSS	Aorta	Aorta
41	chr1:150244800-150245600	Active TSS	Right Atrium	heart
42	chr1:150244800-150245600	Active TSS	Skeletal Muscle Male	skeletal muscle
43	chr1:150244800-150245800	Flanking Active TSS	Fetal Stomach	stomach
44	chr1:150244800-150246000	Active TSS	Brain Hippocampus Middle	brain
45	chr1:150244800-150246400	Active TSS	Rectal Smooth Muscle	rectum
46	chr1:150244800-150246600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
47	chr1:150244800-150250600	Weak transcription	HepG2	liver
48	chr1:150245000-150245600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr1:150245000-150245600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
50	chr1:150245000-150245600	Active TSS	Fetal Lung	lung

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