Variant report

Variant	rs267734
Chromosome Location	chr1:150951477-150951478
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr1:150951395-150952611	HCT-116	colon:	n/a	chr1:150952113-150952122 chr1:150952110-150952128 chr1:150952146-150952162 chr1:150952145-150952163 chr1:150952113-150952126 chr1:150952140-150952161 chr1:150952112-150952133
2	MAX	chr1:150951432-150952214	K562	blood:	n/a	chr1:150951680-150951690
3	CTCF	chr1:150951460-150951610	HCFaa	heart:	n/a	n/a
4	CTCF	chr1:150951440-150951590	HCT-116	colon:	n/a	n/a
5	CTCF	chr1:150951358-150952694	MCF-7	breast:	n/a	chr1:150952113-150952122 chr1:150952110-150952128 chr1:150952146-150952162 chr1:150952145-150952163 chr1:150952113-150952126 chr1:150952140-150952161 chr1:150952112-150952133
6	CTCF	chr1:150951420-150951570	WI-38	lung:	n/a	n/a
7	POLR2A	chr1:150951433-150952367	HL-60	blood:	n/a	n/a
8	CTCF	chr1:150951443-150952664	MCF-7	breast:	n/a	chr1:150952113-150952122 chr1:150952110-150952128 chr1:150952146-150952162 chr1:150952145-150952163 chr1:150952113-150952126 chr1:150952140-150952161 chr1:150952112-150952133
9	POLR2A	chr1:150951387-150952365	PANC-1	pancreas:	n/a	n/a
10	CTCF	chr1:150951460-150951610	AG10803	skin:	n/a	n/a
11	JUN	chr1:150951393-150952642	K562	blood:	n/a	n/a
12	NR2F2	chr1:150951450-150952386	K562	blood:	n/a	n/a
13	CTCF	chr1:150951429-150952703	SK-N-SH	brain:	n/a	chr1:150952113-150952122 chr1:150952110-150952128 chr1:150952146-150952162 chr1:150952145-150952163 chr1:150952113-150952126 chr1:150952140-150952161 chr1:150952112-150952133
14	CTCF	chr1:150951460-150951610	HPAF	blood vessel:	n/a	n/a
15	MAX	chr1:150951403-150952418	A549	lung:	n/a	chr1:150951680-150951690
16	SPI1	chr1:150951444-150952336	HL-60	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:150950114..150952556-chr1:150975284..150977893,2	K562	blood:
2	chr1:150550324..150553500-chr1:150948263..150951593,4	MCF-7	breast:
3	chr1:150949558..150951518-chr1:150957213..150958786,2	K562	blood:
4	chr1:150950305..150952431-chr1:150971107..150975123,3	K562	blood:
5	chr1:150533509..150537383-chr1:150951108..150953934,3	K562	blood:
6	chr1:150897410..150900366-chr1:150947492..150952156,4	K562	blood:
7	chr1:150950614..150952256-chr1:151042194..151044224,2	MCF-7	breast:
8	chr1:150949543..150951625-chr11:11620473..11621993,2	MCF-7	breast:
9	chr1:150950044..150951710-chr4:104823461..104824979,2	MCF-7	breast:
10	chr1:150951084..150953153-chr1:150955362..150957239,2	K562	blood:
11	chr1:150950100..150952046-chr1:150977560..150979538,2	MCF-7	breast:
12	chr1:150949968..150951775-chr4:104823480..104824982,3	MCF-7	breast:
13	chr1:150950075..150953840-chr1:150979246..150981801,5	K562	blood:
14	chr1:150550518..150552449-chr1:150950095..150951828,2	MCF-7	breast:
15	chr1:150950114..150953759-chr1:150976393..150978885,3	K562	blood:
16	chr1:150950574..150954547-chr1:151027400..151032185,6	MCF-7	breast:
17	chr1:150835862..150838203-chr1:150950221..150953041,2	K562	blood:
18	chr1:150892976..150894840-chr1:150949265..150951717,2	K562	blood:
19	chr1:150951440..150951966-chr1:150980502..150981090,2	MCF-7	breast:
20	chr1:150950155..150952613-chr1:151029273..151031994,2	MCF-7	breast:

Variant related genes	Relation type
CERS2	TF binding region
ANXA9	TF binding region
ENSG00000203804	Chromatin interaction
ENSG00000143384	Chromatin interaction
ENSG00000213190	Chromatin interaction
ENSG00000143379	Chromatin interaction
ENSG00000143363	Chromatin interaction
ENSG00000197622	Chromatin interaction
ENSG00000143409	Chromatin interaction
ENSG00000143458	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 12 )

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

rs_ID	r²[population]
rs198325	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs267733	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs267738	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs607518	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001897	chr1:150743271-151241600	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv535158	chr1:150743271-151241600	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv1008496	chr1:150845827-150970656	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
4	nsv522317	chr1:150933723-150974162	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
5	nsv522840	chr1:150933723-151347746	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	169 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Chronic kidney disease	20383146	GWAS catalog

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs267734	LINGO4	cis	cerebellum	SCAN
rs267734	PRKAB2	cis	cerebellum	SCAN
rs267734	SEMA6C	cis	cerebellum	SCAN
rs267734	LYSMD1	cis	lymphoblastoid	seeQTL
rs267734	GABPB2	cis	cerebellum	SCAN
rs267734	MCL1	cis	cerebellum	SCAN
rs267734	CTSK	cis	cerebellum	SCAN
rs267734	SMCP	cis	parietal	SCAN
rs267734	LASS2	cis	lymphoblastoid	seeQTL
rs267734	POLR3GL	cis	cerebellum	SCAN
rs267734	GOLPH3L	cis	cerebellum	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:150948000-150951600	Enhancers	Primary T cells fromperipheralblood	blood
2	chr1:150948000-150951600	Weak transcription	Colonic Mucosa	Colon
3	chr1:150948000-150951600	Enhancers	Fetal Intestine Large	intestine
4	chr1:150948000-150951600	Weak transcription	Fetal Kidney	kidney
5	chr1:150948000-150951600	Weak transcription	Ovary	ovary
6	chr1:150948000-150951800	Weak transcription	Psoas Muscle	Psoas
7	chr1:150948000-150952600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
8	chr1:150948000-150952600	Enhancers	Fetal Intestine Small	intestine
9	chr1:150948200-150951600	Enhancers	Primary T cells from cord blood	blood
10	chr1:150948200-150951800	Weak transcription	Brain Germinal Matrix	brain
11	chr1:150948200-150952000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr1:150948600-150951800	Weak transcription	Fetal Brain Female	brain
13	chr1:150948600-150952800	Enhancers	Placenta	Placenta
14	chr1:150948800-150952000	Enhancers	Lung	lung
15	chr1:150949000-150951600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr1:150949200-150951600	Enhancers	Brain Cingulate Gyrus	brain
17	chr1:150949200-150951800	Enhancers	Fetal Stomach	stomach
18	chr1:150949200-150952600	Enhancers	NH-A	brain
19	chr1:150949600-150951600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr1:150950000-150951600	Enhancers	Primary B cells from peripheral blood	blood
21	chr1:150950000-150951600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
22	chr1:150950000-150951600	Enhancers	Brain Anterior Caudate	brain
23	chr1:150950000-150951600	Enhancers	Brain Substantia Nigra	brain
24	chr1:150950200-150951600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr1:150950200-150951600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr1:150950200-150951600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr1:150950200-150951600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr1:150950200-150951600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr1:150950200-150951600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr1:150950200-150951600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr1:150950200-150951600	Enhancers	Primary hematopoietic stem cells	blood
32	chr1:150950200-150951600	Enhancers	Primary T helper cells PMA-I stimulated	--
33	chr1:150950200-150951600	Enhancers	Primary T helper cells fromperipheralblood	blood
34	chr1:150950200-150951600	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr1:150950200-150951600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr1:150950200-150951600	Enhancers	Adipose Nuclei	Adipose
37	chr1:150950200-150951600	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr1:150950200-150951600	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr1:150950200-150951600	Weak transcription	Esophagus	oesophagus
40	chr1:150950200-150951600	Weak transcription	Gastric	stomach
41	chr1:150950200-150951600	Weak transcription	Left Ventricle	heart
42	chr1:150950200-150951600	Weak transcription	Pancreas	Pancrea
43	chr1:150950200-150951600	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr1:150950200-150951600	Weak transcription	Dnd41	blood
45	chr1:150950200-150951600	Weak transcription	GM12878-XiMat	blood
46	chr1:150950200-150951600	Enhancers	Osteobl	bone
47	chr1:150950200-150951800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
48	chr1:150950200-150951800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr1:150950200-150951800	Weak transcription	Rectal Smooth Muscle	rectum
50	chr1:150950200-150951800	Weak transcription	Right Atrium	heart

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