Variant report

Variant	rs2298161
Chromosome Location	chr1:150237624-150237625
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:150237510-150237749	HepG2	liver:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:150235850..150239142-chr1:150253638..150255727,4	K562	blood:
2	chr1:150206880..150209093-chr1:150235323..150238769,4	MCF-7	breast:
3	chr1:150236930..150239122-chr1:150335854..150338442,2	K562	blood:
4	chr1:150222083..150223904-chr1:150235956..150238749,2	MCF-7	breast:
5	chr1:150227702..150230865-chr1:150236687..150241657,6	K562	blood:

No data

Variant related genes	Relation type
C1orf54	TF binding region
ENSG00000159208	Chromatin interaction
ENSG00000118298	Chromatin interaction
ENSG00000143401	Chromatin interaction
ENSG00000163125	Chromatin interaction
ENSG00000271845	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10888577	0.84[CHD][hapmap];0.87[GIH][hapmap]
rs11205341	0.88[CEU][hapmap]
rs11205354	0.85[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.85[JPT][hapmap];0.82[MEX][hapmap];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12057558	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs12121923	0.82[EUR][1000 genomes]
rs12122277	0.86[CHD][hapmap];0.87[GIH][hapmap]
rs12133235	0.92[CEU][hapmap]
rs1924549	0.92[CEU][hapmap]
rs2038752	0.92[CEU][hapmap]
rs35938158	0.96[CEU][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes]
rs3850839	0.84[CHD][hapmap];0.89[GIH][hapmap]
rs6655935	0.92[CEU][hapmap]
rs6665499	0.88[CEU][hapmap]
rs6676685	0.87[ASN][1000 genomes]
rs6680040	0.88[CEU][hapmap]
rs6681029	0.84[YRI][hapmap]
rs6688118	0.84[YRI][hapmap]
rs7522034	0.92[CEU][hapmap]
rs7548543	0.92[CEU][hapmap]

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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2298161	MRPS21	cis	parietal	SCAN
rs2298161	TNFAIP8L2	cis	cerebellum	SCAN
rs2298161	MRPS21	cis	cerebellum	SCAN
rs2298161	SEC22B	cis	parietal	SCAN
rs2298161	C1orf54	cis	multi-tissue	Pritchard

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:150230800-150239400	Weak transcription	Fetal Brain Male	brain
2	chr1:150230800-150239400	Weak transcription	Right Atrium	heart
3	chr1:150232600-150240400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr1:150233000-150237800	Weak transcription	Colonic Mucosa	Colon
5	chr1:150233000-150239000	Weak transcription	Fetal Kidney	kidney
6	chr1:150233000-150239400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:150233000-150239800	Strong transcription	H1 Cell Line	embryonic stem cell
8	chr1:150233200-150239600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
9	chr1:150233200-150239800	Strong transcription	HUES48 Cell Line	embryonic stem cell
10	chr1:150233200-150240200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr1:150233400-150239400	Strong transcription	Cortex derived primary cultured neurospheres	brain
12	chr1:150233600-150239400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr1:150233600-150239600	Strong transcription	HUES6 Cell Line	embryonic stem cell
14	chr1:150233600-150239800	Strong transcription	H9 Cell Line	embryonic stem cell
15	chr1:150233600-150239800	Strong transcription	HUES64 Cell Line	embryonic stem cell
16	chr1:150233600-150239800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
17	chr1:150233800-150239400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr1:150233800-150239800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
19	chr1:150234000-150238200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr1:150234000-150239800	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr1:150234400-150239200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr1:150234400-150239400	Weak transcription	Fetal Heart	heart
23	chr1:150234800-150239400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr1:150234800-150239800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr1:150235000-150238400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr1:150235000-150238400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr1:150235400-150238000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr1:150235400-150238200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr1:150235400-150239800	Strong transcription	Fetal Stomach	stomach
30	chr1:150235600-150239600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr1:150235600-150239600	Strong transcription	Brain Cingulate Gyrus	brain
32	chr1:150235800-150239400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr1:150235800-150239400	Strong transcription	Stomach Smooth Muscle	stomach
34	chr1:150235800-150239600	Strong transcription	Fetal Muscle Leg	muscle
35	chr1:150235800-150239800	Weak transcription	Small Intestine	intestine
36	chr1:150236000-150238200	Strong transcription	Spleen	Spleen
37	chr1:150236000-150239400	Strong transcription	Lung	lung
38	chr1:150236000-150239600	Strong transcription	Right Ventricle	heart
39	chr1:150236000-150239800	Strong transcription	Primary T cells from cord blood	blood
40	chr1:150236200-150237800	Weak transcription	NHEK	skin
41	chr1:150236200-150238400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr1:150236200-150238800	Weak transcription	Hela-S3	cervix
43	chr1:150236200-150239600	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr1:150236200-150239800	Weak transcription	Stomach Mucosa	stomach
45	chr1:150236600-150238000	Genic enhancers	Primary neutrophils fromperipheralblood	blood
46	chr1:150236600-150238000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr1:150236600-150238600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
48	chr1:150236600-150239400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr1:150236600-150239600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr1:150236600-150239600	Strong transcription	Adipose Nuclei	Adipose

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