Variant report

Variant	rs3755182
Chromosome Location	chr2:211342138-211342139
allele	A/C
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	POLR2A	chr2:211340622-211343315	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr2:211342096-211342595	HepG2	liver:	n/a	n/a
3	RFX5	chr2:211340284-211342739	SK-N-SH	brain:	n/a	chr2:211341503-211341512
4	MAX	chr2:211342093-211342553	SK-N-SH	brain:	n/a	n/a
5	POLR2A	chr2:211341976-211342617	Hela-S3	cervix:	n/a	n/a
6	MYBL2	chr2:211342092-211342598	HepG2	liver:	n/a	n/a
7	TBL1XR1	chr2:211342119-211342554	K562	blood:	n/a	n/a
8	MYC	chr2:211341268-211342524	K562	blood:	n/a	n/a
9	TBP	chr2:211342115-211342621	Hela-S3	cervix:	n/a	n/a
10	MAZ	chr2:211342039-211342502	IMR90	lung:	n/a	n/a
11	POLR2A	chr2:211342099-211342600	HepG2	liver:	n/a	n/a
12	SP1	chr2:211342010-211342732	HCT-116	colon:	n/a	n/a
13	POLR2A	chr2:211342116-211342517	K562	blood:	n/a	n/a
14	MXI1	chr2:211340118-211342969	SK-N-SH	brain:	n/a	n/a
15	POLR2A	chr2:211341957-211342746	U87	brain:	n/a	n/a
16	POLR2A	chr2:211342076-211342590	U87	brain:	n/a	n/a
17	EGR1	chr2:211342124-211342495	H1-hESC	embryonic stem cell:	n/a	n/a
18	MYBL2	chr2:211341953-211342718	HepG2	liver:	n/a	n/a
19	MAZ	chr2:211342053-211342541	HepG2	liver:	n/a	n/a
20	HEY1	chr2:211342047-211342610	HepG2	liver:	n/a	n/a
21	JUN	chr2:211342106-211342612	K562	blood:	n/a	n/a
22	POLR2A	chr2:211342102-211342551	HepG2	liver:	n/a	n/a
23	MAZ	chr2:211341103-211342568	GM12878	blood:	n/a	chr2:211341219-211341229
24	ELF1	chr2:211342111-211342693	HCT-116	colon:	n/a	n/a
25	POLR2A	chr2:211341963-211342740	U87	brain:	n/a	n/a
26	POLR2A	chr2:211342069-211342461	ProgFib	skin:	n/a	n/a
27	POLR2A	chr2:211342084-211342645	HCT-116	colon:	n/a	n/a
28	POLR2A	chr2:211342049-211342603	SK-N-SH	brain:	n/a	n/a

Variant related genes	Relation type
LANCL1	TF binding region
CPS1	TF binding region

Extended variants
information (count: 50 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10932334	0.80[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.91[MEX][hapmap];0.83[MKK][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10932339	0.89[CEU][hapmap];0.82[YRI][hapmap]
rs12464878	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12474078	0.86[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.92[MKK][hapmap];0.87[TSI][hapmap];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12618926	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12623942	0.90[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs1396954	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1509820	0.80[ASW][hapmap];0.89[CEU][hapmap];0.91[YRI][hapmap]
rs17552879	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2007748	0.89[CEU][hapmap];0.91[YRI][hapmap]
rs2042049	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.96[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2287417	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2287418	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2287419	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2287420	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2287421	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2287422	0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2370948	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3732055	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3770685	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs3770687	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3770690	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3770691	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3856340	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3856342	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs3856343	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3856344	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3856345	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3856346	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3856347	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3856348	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3856349	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4672575	0.82[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs4672577	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4673530	0.99[ASN][1000 genomes]
rs4673531	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4673532	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4673533	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62203668	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62203669	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62203670	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62203672	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62203673	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62203674	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62203675	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6727682	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7569252	0.84[ASN][1000 genomes]
rs7580046	0.89[CEU][hapmap];0.91[YRI][hapmap]
rs7603241	0.89[CEU][hapmap];0.91[YRI][hapmap]

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	esv3398091	chr2:211315261-211634200	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs3755182	CPS1	cis	cerebellum	SCAN
rs3755182	CPS1	cis	Artery Tibial	GTEx
rs3755182	LANCL1	cis	cerebellum	SCAN
rs3755182	CPS1	cis	Adipose Subcutaneous	GTEx
rs3755182	CPS1	cis	lung	GTEx
rs3755182	LANCL1	cis	multi-tissue	Pritchard
rs3755182	LANCL1	cis	parietal	SCAN

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:211339800-211342600	Active TSS	Brain Angular Gyrus	brain
2	chr2:211339800-211342800	Active TSS	A549	lung
3	chr2:211340000-211342800	Active TSS	Brain Anterior Caudate	brain
4	chr2:211340200-211342600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr2:211340200-211342600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr2:211340200-211342800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr2:211340200-211342800	Active TSS	Hela-S3	cervix
8	chr2:211340200-211343000	Active TSS	Stomach Smooth Muscle	stomach
9	chr2:211340200-211343000	Active TSS	HSMMtube	muscle
10	chr2:211340200-211343200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr2:211340400-211342400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr2:211340400-211342400	Active TSS	Brain Cingulate Gyrus	brain
13	chr2:211340400-211342400	Active TSS	Skeletal Muscle Female	skeletal muscle
14	chr2:211340400-211342600	Active TSS	iPS-15b Cell Line	embryonic stem cell
15	chr2:211340400-211342600	Active TSS	Brain Inferior Temporal Lobe	brain
16	chr2:211340400-211342600	Active TSS	Right Ventricle	heart
17	chr2:211340400-211342800	Active TSS	H1 Cell Line	embryonic stem cell
18	chr2:211340400-211342800	Active TSS	Aorta	Aorta
19	chr2:211340400-211342800	Active TSS	NHDF-Ad	bronchial
20	chr2:211340400-211343000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr2:211340400-211343000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr2:211340400-211343000	Active TSS	Right Atrium	heart
23	chr2:211340400-211343000	Active TSS	GM12878-XiMat	blood
24	chr2:211340400-211343000	Active TSS	HSMM	muscle
25	chr2:211340400-211343200	Active TSS	ES-I3 Cell Line	embryonic stem cell
26	chr2:211340400-211343200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr2:211340400-211343200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr2:211340400-211343200	Active TSS	Ovary	ovary
29	chr2:211340400-211343200	Active TSS	NHLF	lung
30	chr2:211340400-211343400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr2:211340600-211342200	Active TSS	Primary T cells fromperipheralblood	blood
32	chr2:211340600-211342400	Active TSS	Rectal Mucosa Donor 29	rectum
33	chr2:211340600-211342400	Bivalent/Poised TSS	HepG2	liver
34	chr2:211340600-211342600	Active TSS	H9 Cell Line	embryonic stem cell
35	chr2:211340600-211342600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr2:211340600-211342600	Active TSS	Fetal Intestine Small	intestine
37	chr2:211340600-211342800	Active TSS	Brain Hippocampus Middle	brain
38	chr2:211340600-211343000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr2:211340600-211343200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr2:211340600-211343200	Active TSS	Duodenum Smooth Muscle	Duodenum
41	chr2:211340600-211343400	Active TSS	K562	blood
42	chr2:211340800-211342200	Active TSS	Skeletal Muscle Male	skeletal muscle
43	chr2:211340800-211342600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
44	chr2:211340800-211342600	Active TSS	Left Ventricle	heart
45	chr2:211340800-211342800	Active TSS	Adipose Nuclei	Adipose
46	chr2:211340800-211342800	Active TSS	Duodenum Mucosa	Duodenum
47	chr2:211340800-211342800	Active TSS	Fetal Lung	lung
48	chr2:211340800-211342800	Active TSS	NHEK	skin
49	chr2:211340800-211343000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr2:211340800-211343000	Active TSS	NH-A	brain

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