Variant report

Variant	rs34511570
Chromosome Location	chr2:55463103-55463104
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:85)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:85 , 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	chr2:55462852-55463121	SK-N-SH	brain:	n/a	n/a
11	POLR2A	chr2:55462966-55463147	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	POLR2A	chr2:55462952-55463708	K562	blood:	n/a	n/a
17	TEAD4	chr2:55462957-55463735	K562	blood:	n/a	n/a
18	NFATC1	chr2:55462847-55464771	GM12878	blood:	n/a	n/a
19	POLR2A	chr2:55461373-55464681	HepG2	liver:	n/a	n/a
20	POLR2A	chr2:55459164-55464717	GM12878	blood:	n/a	n/a
21	POLR2A	chr2:55462734-55464756	U87	brain:	n/a	n/a
22	POLR2A	chr2:55458775-55464779	Hela-S3	cervix:	n/a	n/a
23	POLR2A	chr2:55458974-55464629	K562	blood:	n/a	n/a
24	POLR2A	chr2:55462947-55463257	HepG2	liver:	n/a	n/a
25	POLR2A	chr2:55458800-55464614	K562	blood:	n/a	n/a
26	BCL3	chr2:55462736-55464796	A549	lung:	n/a	chr2:55464104-55464113
27	POLR2A	chr2:55462728-55464725	HUVEC	blood vessel:	n/a	n/a
28	POLR2A	chr2:55462929-55463880	K562	blood:	n/a	n/a
29	HEY1	chr2:55462435-55463896	HepG2	liver:	n/a	n/a
30	POLR2A	chr2:55462839-55464612	IMR90	lung:	n/a	n/a
31	POLR2A	chr2:55462208-55464000	H1-hESC	embryonic stem cell:	n/a	n/a
32	HEY1	chr2:55462185-55464659	HepG2	liver:	n/a	n/a
33	POLR2A	chr2:55462683-55464637	H1-hESC	embryonic stem cell:	n/a	n/a
34	POLR2A	chr2:55462669-55464686	PANC-1	pancreas:	n/a	n/a
35	POLR2A	chr2:55458988-55464662	GM12878	blood:	n/a	n/a
36	POLR2A	chr2:55462711-55464505	HepG2	liver:	n/a	n/a
37	PML	chr2:55462666-55463750	K562	blood:	n/a	n/a
38	POLR2A	chr2:55461469-55464573	K562	blood:	n/a	n/a
39	POLR2A	chr2:55462742-55464544	GM19099	blood:	n/a	n/a
40	JUND	chr2:55463020-55463137	H1-hESC	embryonic stem cell:	n/a	n/a
41	POLR2A	chr2:55462758-55463110	ECC-1	luminal epithelium:	n/a	n/a
42	POLR2A	chr2:55458860-55465354	PFSK-1	brain:	n/a	n/a
43	POLR2A	chr2:55458989-55464724	PANC-1	pancreas:	n/a	n/a
44	POLR2A	chr2:55458966-55464603	GM12892	blood:	n/a	n/a
45	POLR2A	chr2:55459024-55464715	GM18505	blood:	n/a	n/a
46	POLR2A	chr2:55462273-55464697	HUVEC	blood vessel:	n/a	n/a
47	ZNF384	chr2:55463038-55463308	K562	blood:	n/a	n/a
48	POLR2A	chr2:55462955-55463397	HUVEC	blood vessel:	n/a	n/a
49	POLR2A	chr2:55458733-55465490	Hela-S3	cervix:	n/a	n/a
50	MTA3	chr2:55462692-55464647	GM12878	blood:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:55274511..55278444-chr2:55462893..55465890,4	K562	blood:
2	chr2:55228095..55231014-chr2:55462298..55463930,2	MCF-7	breast:
3	chr2:55462241..55464416-chr2:55656583..55659722,3	MCF-7	breast:
4	chr2:55457538..55465596-chr2:55493335..55497971,13	MCF-7	breast:
5	chr2:55462896..55465238-chr2:55491054..55493846,2	MCF-7	breast:
6	chr2:55275648..55277729-chr2:55462893..55465890,2	K562	blood:
7	chr2:55461063..55464036-chr2:55678930..55681673,2	MCF-7	breast:
8	chr2:55462245..55463992-chr2:55494868..55496568,2	K562	blood:

No data

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

Extended variants
information (count: 34 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10200120	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1056445	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs11357	0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11692206	0.84[EUR][1000 genomes]
rs12052613	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12615414	0.88[EUR][1000 genomes]
rs12988617	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12997656	0.84[EUR][1000 genomes]
rs13021163	0.84[EUR][1000 genomes]
rs17852670	0.92[ASN][1000 genomes]
rs2576711	0.89[AFR][1000 genomes]
rs2576712	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2576721	0.88[AFR][1000 genomes]
rs2589080	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2589092	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs2589093	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs2589096	0.87[AFR][1000 genomes]
rs2589100	0.85[ASN][1000 genomes]
rs2864826	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2917779	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2920967	0.85[ASN][1000 genomes]
rs34348115	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4435493	0.93[ASN][1000 genomes]
rs55997390	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs56039135	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6545480	0.83[ASN][1000 genomes]
rs6706815	0.93[ASN][1000 genomes]
rs71414550	0.84[EUR][1000 genomes]
rs72799507	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7597293	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs934709	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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
3	nsv961777	chr2:55461976-55463347	Transcr. at gene 5' and 3' Strong transcription Genic enhancers Weak transcription Active TSS Enhancers	TF binding region Chromatin interactive region miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs34511570	CLHC1	cis	Artery Tibial	GTEx
rs34511570	FLJ31438	Cis_1M	lymphoblastoid	RTeQTL
rs34511570	CLHC1	cis	Adipose Subcutaneous	GTEx
rs34511570	CLHC1	cis	Esophagus Muscularis	GTEx
rs34511570	C2orf63	cis	multi-tissue	Pritchard
rs34511570	LOC388720///RPS27A	Cis_1M	lymphoblastoid	RTeQTL
rs34511570	CLHC1	cis	Nerve Tibial	GTEx
rs34511570	MTIF2	cis	Nerve Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55460000-55463400	Transcr. at gene 5' and 3'	K562	blood
2	chr2:55460600-55463400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr2:55460600-55463800	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
4	chr2:55461000-55464600	Strong transcription	ES-I3 Cell Line	embryonic stem cell
5	chr2:55461000-55470200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr2:55461200-55463200	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
7	chr2:55461200-55463200	Genic enhancers	Cortex derived primary cultured neurospheres	brain
8	chr2:55461200-55463600	Strong transcription	Rectal Smooth Muscle	rectum
9	chr2:55461200-55463600	Strong transcription	Thymus	Thymus
10	chr2:55461200-55464600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr2:55461200-55464800	Strong transcription	Skeletal Muscle Male	skeletal muscle
12	chr2:55461400-55463400	Strong transcription	Ovary	ovary
13	chr2:55461400-55463600	Strong transcription	Brain Substantia Nigra	brain
14	chr2:55461400-55464000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr2:55461400-55464400	Strong transcription	Brain Anterior Caudate	brain
16	chr2:55461400-55464400	Strong transcription	Fetal Lung	lung
17	chr2:55461400-55466600	Strong transcription	Primary neutrophils fromperipheralblood	blood
18	chr2:55461400-55477600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr2:55461600-55463200	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr2:55461600-55463400	Strong transcription	Lung	lung
21	chr2:55461600-55463600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr2:55461600-55463600	Strong transcription	Left Ventricle	heart
23	chr2:55461600-55463800	Strong transcription	H9 Cell Line	embryonic stem cell
24	chr2:55461600-55464400	Strong transcription	Colonic Mucosa	Colon
25	chr2:55461600-55464400	Strong transcription	Stomach Smooth Muscle	stomach
26	chr2:55461600-55464600	Strong transcription	Placenta	Placenta
27	chr2:55461600-55466600	Strong transcription	Fetal Intestine Large	intestine
28	chr2:55461600-55466600	Strong transcription	HSMMtube	muscle
29	chr2:55461600-55467400	Strong transcription	Adipose Nuclei	Adipose
30	chr2:55461600-55467800	Strong transcription	Primary monocytes fromperipheralblood	blood
31	chr2:55461600-55469400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr2:55461600-55471600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr2:55461600-55477000	Strong transcription	Fetal Muscle Leg	muscle
34	chr2:55461600-55481600	Strong transcription	Fetal Thymus	thymus
35	chr2:55461600-55495400	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr2:55461600-55495400	Weak transcription	Stomach Mucosa	stomach
37	chr2:55461800-55463200	Strong transcription	Colon Smooth Muscle	Colon
38	chr2:55461800-55463200	Weak transcription	Psoas Muscle	Psoas
39	chr2:55461800-55463600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr2:55461800-55464000	Strong transcription	Fetal Kidney	kidney
41	chr2:55461800-55464400	Strong transcription	Rectal Mucosa Donor 31	rectum
42	chr2:55461800-55464400	Strong transcription	NHLF	lung
43	chr2:55461800-55464600	Strong transcription	Brain Inferior Temporal Lobe	brain
44	chr2:55461800-55464600	Strong transcription	HSMM	muscle
45	chr2:55461800-55464800	Strong transcription	HUES6 Cell Line	embryonic stem cell
46	chr2:55461800-55464800	Strong transcription	Fetal Muscle Trunk	muscle
47	chr2:55461800-55465200	Weak transcription	Fetal Stomach	stomach
48	chr2:55461800-55465400	Strong transcription	H1 Cell Line	embryonic stem cell
49	chr2:55461800-55465400	Strong transcription	Sigmoid Colon	Sigmoid Colon
50	chr2:55461800-55465800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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