Variant report

Variant	rs56039135
Chromosome Location	chr2:55463576-55463577
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:88)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:88 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:55458744-55464800	K562	blood:	n/a	n/a
2	POLR2A	chr2:55462090-55464756	U87	brain:	n/a	n/a
3	POLR2A	chr2:55462401-55465841	HepG2	liver:	n/a	n/a
4	POLR2A	chr2:55458959-55464692	GM12878	blood:	n/a	n/a
5	POLR2A	chr2:55458747-55464848	U87	brain:	n/a	n/a
6	POLR2A	chr2:55462733-55463621	HL-60	blood:	n/a	n/a
7	POLR2A	chr2:55462162-55463984	GM12891	blood:	n/a	n/a
8	POLR2A	chr2:55462679-55464540	HCT-116	colon:	n/a	n/a
9	POLR2A	chr2:55458731-55465585	GM12891	blood:	n/a	n/a
10	POLR2A	chr2:55463131-55464619	ECC-1	luminal epithelium:	n/a	n/a
11	TAF7	chr2:55463517-55463915	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr2:55458627-55465420	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr2:55462398-55463833	H1-hESC	embryonic stem cell:	n/a	n/a
14	POLR2A	chr2:55458643-55463921	SK-N-MC	brain:	n/a	n/a
15	POLR2A	chr2:55458760-55464736	HepG2	liver:	n/a	n/a
16	TAL1	chr2:55463258-55463695	K562	blood:	n/a	n/a
17	POLR2A	chr2:55462952-55463708	K562	blood:	n/a	n/a
18	TEAD4	chr2:55462957-55463735	K562	blood:	n/a	n/a
19	NFATC1	chr2:55462847-55464771	GM12878	blood:	n/a	n/a
20	POLR2A	chr2:55461373-55464681	HepG2	liver:	n/a	n/a
21	CHD2	chr2:55463202-55463732	H1-hESC	embryonic stem cell:	n/a	n/a
22	POLR2A	chr2:55459164-55464717	GM12878	blood:	n/a	n/a
23	NFATC1	chr2:55463122-55464729	GM12878	blood:	n/a	n/a
24	POLR2A	chr2:55462734-55464756	U87	brain:	n/a	n/a
25	POLR2A	chr2:55458775-55464779	Hela-S3	cervix:	n/a	n/a
26	ATF2	chr2:55463140-55464509	H1-hESC	embryonic stem cell:	n/a	n/a
27	POLR2A	chr2:55463513-55463589	GM12878	blood:	n/a	n/a
28	POLR2A	chr2:55458974-55464629	K562	blood:	n/a	n/a
29	POLR2A	chr2:55458800-55464614	K562	blood:	n/a	n/a
30	BCL3	chr2:55462736-55464796	A549	lung:	n/a	chr2:55464104-55464113
31	POLR2A	chr2:55463483-55463758	HUVEC	blood vessel:	n/a	n/a
32	POLR2A	chr2:55462728-55464725	HUVEC	blood vessel:	n/a	n/a
33	POLR2A	chr2:55462929-55463880	K562	blood:	n/a	n/a
34	HEY1	chr2:55462435-55463896	HepG2	liver:	n/a	n/a
35	POLR2A	chr2:55462839-55464612	IMR90	lung:	n/a	n/a
36	POLR2A	chr2:55462208-55464000	H1-hESC	embryonic stem cell:	n/a	n/a
37	HEY1	chr2:55462185-55464659	HepG2	liver:	n/a	n/a
38	POLR2A	chr2:55462683-55464637	H1-hESC	embryonic stem cell:	n/a	n/a
39	POLR2A	chr2:55462669-55464686	PANC-1	pancreas:	n/a	n/a
40	POLR2A	chr2:55458988-55464662	GM12878	blood:	n/a	n/a
41	POLR2A	chr2:55462711-55464505	HepG2	liver:	n/a	n/a
42	PML	chr2:55462666-55463750	K562	blood:	n/a	n/a
43	POLR2A	chr2:55461469-55464573	K562	blood:	n/a	n/a
44	POLR2A	chr2:55462742-55464544	GM19099	blood:	n/a	n/a
45	MTA3	chr2:55463315-55463882	GM12878	blood:	n/a	n/a
46	POLR2A	chr2:55458860-55465354	PFSK-1	brain:	n/a	n/a
47	POLR2A	chr2:55458989-55464724	PANC-1	pancreas:	n/a	n/a
48	POLR2A	chr2:55458966-55464603	GM12892	blood:	n/a	n/a
49	POLR2A	chr2:55459024-55464715	GM18505	blood:	n/a	n/a
50	POLR2A	chr2:55462273-55464697	HUVEC	blood vessel:	n/a	n/a

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:55463258..55466209-chr2:55509433..55511989,3	MCF-7	breast:
2	chr2:55463171..55466180-chr2:55659869..55661423,3	MCF-7	breast:
3	chr11:71934525..71935309-chr2:55463107..55463893,2	Hela-S3	cervix:
4	chr2:55274511..55278444-chr2:55462893..55465890,4	K562	blood:
5	chr2:55228095..55231014-chr2:55462298..55463930,2	MCF-7	breast:
6	chr2:55462241..55464416-chr2:55656583..55659722,3	MCF-7	breast:
7	chr2:55457538..55465596-chr2:55493335..55497971,13	MCF-7	breast:
8	chr2:55462896..55465238-chr2:55491054..55493846,2	MCF-7	breast:
9	chr2:55275648..55277729-chr2:55462893..55465890,2	K562	blood:
10	chr2:55461063..55464036-chr2:55678930..55681673,2	MCF-7	breast:
11	chr2:55462245..55463992-chr2:55494868..55496568,2	K562	blood:

No data

Variant related genes	Relation type
CLHC1	TF binding region
ENSG00000115310	Chromatin interaction
ENSG00000165458	Chromatin interaction
ENSG00000162997	Chromatin interaction
ENSG00000085760	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10200120	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1056445	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11357	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11692206	0.85[EUR][1000 genomes]
rs12052613	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12615414	0.89[EUR][1000 genomes]
rs12988617	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12997656	0.83[EUR][1000 genomes]
rs13021163	0.83[EUR][1000 genomes]
rs17852670	0.94[ASN][1000 genomes]
rs2576711	0.85[AFR][1000 genomes]
rs2576712	0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2576719	0.85[AFR][1000 genomes]
rs2576721	0.85[AFR][1000 genomes]
rs2589080	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2589092	0.87[AMR][1000 genomes]
rs2589093	0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2589096	0.84[AFR][1000 genomes]
rs2589100	0.82[ASN][1000 genomes]
rs2864819	0.81[ASN][1000 genomes]
rs2864826	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2917779	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2920967	0.83[ASN][1000 genomes]
rs34348115	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34511570	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4435493	0.94[ASN][1000 genomes]
rs55997390	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6545480	0.85[ASN][1000 genomes]
rs6706815	0.94[ASN][1000 genomes]
rs71414550	0.85[EUR][1000 genomes]
rs72799507	0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7597293	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs934709	0.90[ASN][1000 genomes]

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	nsv522016	chr2:55404794-55560298	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	esv3348896	chr2:55429540-55498552	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs56039135	CLHC1	cis	Artery Tibial	GTEx
rs56039135	FLJ31438	Cis_1M	lymphoblastoid	RTeQTL
rs56039135	LOC388720///RPS27A	Cis_1M	lymphoblastoid	RTeQTL
rs56039135	C2orf63	cis	multi-tissue	Pritchard
rs56039135	CLHC1	cis	Adipose Subcutaneous	GTEx
rs56039135	CLHC1	cis	Muscle Skeletal	GTEx
rs56039135	CLHC1	cis	Esophagus Muscularis	GTEx
rs56039135	MTIF2	cis	Nerve Tibial	GTEx
rs56039135	CLHC1	cis	Nerve Tibial	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55460600-55463800	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
2	chr2:55461000-55464600	Strong transcription	ES-I3 Cell Line	embryonic stem cell
3	chr2:55461000-55470200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr2:55461200-55463600	Strong transcription	Rectal Smooth Muscle	rectum
5	chr2:55461200-55463600	Strong transcription	Thymus	Thymus
6	chr2:55461200-55464600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr2:55461200-55464800	Strong transcription	Skeletal Muscle Male	skeletal muscle
8	chr2:55461400-55463600	Strong transcription	Brain Substantia Nigra	brain
9	chr2:55461400-55464000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr2:55461400-55464400	Strong transcription	Brain Anterior Caudate	brain
11	chr2:55461400-55464400	Strong transcription	Fetal Lung	lung
12	chr2:55461400-55466600	Strong transcription	Primary neutrophils fromperipheralblood	blood
13	chr2:55461400-55477600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr2:55461600-55463600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr2:55461600-55463600	Strong transcription	Left Ventricle	heart
16	chr2:55461600-55463800	Strong transcription	H9 Cell Line	embryonic stem cell
17	chr2:55461600-55464400	Strong transcription	Colonic Mucosa	Colon
18	chr2:55461600-55464400	Strong transcription	Stomach Smooth Muscle	stomach
19	chr2:55461600-55464600	Strong transcription	Placenta	Placenta
20	chr2:55461600-55466600	Strong transcription	Fetal Intestine Large	intestine
21	chr2:55461600-55466600	Strong transcription	HSMMtube	muscle
22	chr2:55461600-55467400	Strong transcription	Adipose Nuclei	Adipose
23	chr2:55461600-55467800	Strong transcription	Primary monocytes fromperipheralblood	blood
24	chr2:55461600-55469400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr2:55461600-55471600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr2:55461600-55477000	Strong transcription	Fetal Muscle Leg	muscle
27	chr2:55461600-55481600	Strong transcription	Fetal Thymus	thymus
28	chr2:55461600-55495400	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr2:55461600-55495400	Weak transcription	Stomach Mucosa	stomach
30	chr2:55461800-55463600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr2:55461800-55464000	Strong transcription	Fetal Kidney	kidney
32	chr2:55461800-55464400	Strong transcription	Rectal Mucosa Donor 31	rectum
33	chr2:55461800-55464400	Strong transcription	NHLF	lung
34	chr2:55461800-55464600	Strong transcription	Brain Inferior Temporal Lobe	brain
35	chr2:55461800-55464600	Strong transcription	HSMM	muscle
36	chr2:55461800-55464800	Strong transcription	HUES6 Cell Line	embryonic stem cell
37	chr2:55461800-55464800	Strong transcription	Fetal Muscle Trunk	muscle
38	chr2:55461800-55465200	Weak transcription	Fetal Stomach	stomach
39	chr2:55461800-55465400	Strong transcription	H1 Cell Line	embryonic stem cell
40	chr2:55461800-55465400	Strong transcription	Sigmoid Colon	Sigmoid Colon
41	chr2:55461800-55465800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr2:55461800-55466600	Strong transcription	Primary hematopoietic stem cells	blood
43	chr2:55461800-55467400	Strong transcription	Liver	Liver
44	chr2:55461800-55467400	Strong transcription	Monocytes-CD14+_RO01746	blood
45	chr2:55461800-55472400	Weak transcription	Gastric	stomach
46	chr2:55461800-55472400	Weak transcription	Right Ventricle	heart
47	chr2:55461800-55474400	Strong transcription	Primary T cells fromperipheralblood	blood
48	chr2:55461800-55493400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr2:55461800-55495000	Weak transcription	Fetal Brain Male	brain
50	chr2:55462000-55463600	Strong transcription	Primary T killer naive cells fromperipheralblood	blood

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