Variant report

Variant	rs10173492
Chromosome Location	chr2:11485457-11485458
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:268)
CpG islands
(count:61)
Chromatin interactive
region (count:18)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:268 , 50 per page) page: 1 2 3 4 5 6

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EP300	chr2:11484623-11485904	K562	blood:	n/a	chr2:11485239-11485248
2	CHD2	chr2:11484906-11485631	HepG2	liver:	n/a	n/a
3	CHD2	chr2:11485214-11485720	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr2:11484391-11485980	PANC-1	pancreas:	n/a	n/a
5	JUND	chr2:11484750-11485505	A549	lung:	n/a	chr2:11485174-11485185
6	MAZ	chr2:11482527-11485966	IMR90	lung:	n/a	chr2:11484107-11484117
7	MAX	chr2:11483578-11485610	ECC-1	luminal epithelium:	n/a	chr2:11484107-11484117
8	TEAD4	chr2:11484961-11485737	K562	blood:	n/a	n/a
9	CHD2	chr2:11483659-11485828	Hela-S3	cervix:	n/a	chr2:11484574-11484584
10	EP300	chr2:11485357-11485793	T-47D	breast:	n/a	n/a
11	POLR2A	chr2:11483825-11485635	HUVEC	blood vessel:	n/a	n/a
12	SIN3AK20	chr2:11483595-11485509	PANC-1	pancreas:	n/a	n/a
13	NR2F2	chr2:11485327-11485960	K562	blood:	n/a	n/a
14	TEAD4	chr2:11484861-11485866	A549	lung:	n/a	n/a
15	MAX	chr2:11482548-11486084	A549	lung:	n/a	chr2:11484107-11484117
16	BACH1	chr2:11484900-11485494	H1-hESC	embryonic stem cell:	n/a	n/a
17	MXI1	chr2:11481913-11486311	SK-N-SH	brain:	n/a	n/a
18	MAX	chr2:11482699-11485758	HepG2	liver:	n/a	chr2:11484107-11484117
19	GATA2	chr2:11485292-11485871	HUVEC	blood vessel:	n/a	n/a
20	POLR2A	chr2:11483555-11485468	H1-neurons	neurons:	n/a	n/a
21	RXRA	chr2:11484652-11485739	HepG2	liver:	n/a	chr2:11485242-11485262
22	MYC	chr2:11483622-11485498	K562	blood:	n/a	chr2:11484107-11484117
23	TEAD4	chr2:11484822-11485767	A549	lung:	n/a	n/a
24	BRCA1	chr2:11484901-11485468	HepG2	liver:	n/a	n/a
25	POLR2A	chr2:11482729-11486472	MCF10A-Er-Src	breast:	n/a	n/a
26	POLR2A	chr2:11484566-11485845	GM12878	blood:	n/a	n/a
27	POLR2A	chr2:11484494-11485917	K562	blood:	n/a	n/a
28	MAZ	chr2:11482539-11485760	HepG2	liver:	n/a	chr2:11484107-11484117
29	POLR2A	chr2:11482788-11486262	MCF10A-Er-Src	breast:	n/a	n/a
30	POLR2A	chr2:11482618-11486449	Hela-S3	cervix:	n/a	n/a
31	CHD2	chr2:11484850-11485730	K562	blood:	n/a	n/a
32	TEAD4	chr2:11484941-11486000	HCT-116	colon:	n/a	n/a
33	TCF7L2	chr2:11485019-11485816	Hela-S3	cervix:	n/a	n/a
34	MBD4	chr2:11484737-11485900	HepG2	liver:	n/a	n/a
35	TEAD4	chr2:11485071-11485750	H1-hESC	embryonic stem cell:	n/a	n/a
36	TAF1	chr2:11484530-11485800	Hela-S3	cervix:	n/a	n/a
37	POLR2A	chr2:11484474-11485950	SK-N-SH	brain:	n/a	n/a
38	JUND	chr2:11484552-11485971	SK-N-SH	brain:	n/a	chr2:11485174-11485185
39	MXI1	chr2:11484687-11485911	Hela-S3	cervix:	n/a	n/a
40	E2F1	chr2:11484372-11485956	Hela-S3	cervix:	n/a	chr2:11484485-11484500 chr2:11485047-11485056
41	REST	chr2:11484625-11485532	H1-neurons	neurons:	n/a	n/a
42	POLR2A	chr2:11482554-11486380	HepG2	liver:	n/a	n/a
43	POLR2A	chr2:11483578-11485833	Hela-S3	cervix:	n/a	n/a
44	HA-E2F1	chr2:11483698-11485737	MCF-7	breast:	n/a	chr2:11484485-11484500 chr2:11485047-11485056 chr2:11484103-11484113
45	MAFK	chr2:11484861-11485861	Hela-S3	cervix:	n/a	chr2:11485177-11485186
46	REST	chr2:11483545-11485822	HepG2	liver:	n/a	chr2:11484001-11484014
47	POLR2A	chr2:11484619-11485655	U87	brain:	n/a	n/a
48	SRF	chr2:11484601-11486069	HCT-116	colon:	n/a	chr2:11485114-11485124 chr2:11485621-11485639 chr2:11485622-11485640 chr2:11485054-11485064
49	TEAD4	chr2:11484879-11485842	SK-N-SH	brain:	n/a	n/a
50	CEBPB	chr2:11485448-11485888	IMR90	lung:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr2:11485413-11485463	T-47D	breast:	n/a
2	chr2:11485413-11485463	HRCEpiC	kidney:	n/a
3	chr2:11485413-11485463	GM12892	blood:	n/a
4	chr2:11485413-11485463	Hela-S3	cervix:	n/a
5	chr2:11485413-11485463	AG04449	skin:	fetal
6	chr2:11485413-11485463	NHDF-neo	bronchial:	n/a
7	chr2:11485413-11485463	GM19239	blood:	n/a
8	chr2:11485413-11485463	HMEC	breast:	n/a
9	chr2:11485413-11485463	HepG2	liver:	n/a
10	chr2:11485413-11485463	HAEpiC	amniotic membrane:	n/a
11	chr2:11485413-11485463	HPAEpiC	pulmonary alveolar:	n/a
12	chr2:11485413-11485463	K562	blood:	n/a
13	chr2:11485413-11485463	CMK	blood:	n/a
14	chr2:11485413-11485463	AG10803	skin:	n/a
15	chr2:11485413-11485463	AG09309	skin:	n/a
16	chr2:11485413-11485463	HRPEpiC	eye:	n/a
17	chr2:11485413-11485463	AG09319	gingival:	n/a
18	chr2:11485413-11485463	PrEC	prostate:	n/a
19	chr2:11485413-11485463	SK-N-MC	brain:	n/a
20	chr2:11485413-11485463	NT2-D1	testis:	n/a
21	chr2:11485413-11485463	HCF	heart:	n/a
22	chr2:11485413-11485463	PFSK-1	brain:	n/a
23	chr2:11485413-11485463	ECC-1	luminal epithelium:	n/a
24	chr2:11485413-11485463	SK-N-SH_RA	brain:	n/a
25	chr2:11485413-11485463	BE2_C	brain:	n/a
26	chr2:11485413-11485463	HCT-116	colon:	n/a
27	chr2:11485413-11485463	HL-60	blood:	n/a
28	chr2:11485413-11485463	AG04450	lung:	fetal
29	chr2:11485413-11485463	GM06990	blood:	n/a
30	chr2:11485413-11485463	Jurkat	blood:	n/a
31	chr2:11485413-11485463	ovcar-3	ovarian:	n/a
32	chr2:11485413-11485463	ProgFib	skin:	n/a
33	chr2:11485413-11485463	HCPEpiC	choroid plexus:	n/a
34	chr2:11485413-11485463	SAEC	small airway:	n/a
35	chr2:11485413-11485463	IMR90	lung:	fetal
36	chr2:11485413-11485463	HCM	heart:	n/a
37	chr2:11485413-11485463	H1-hESC	embryonic stem cell:	embryo
38	chr2:11485413-11485463	RPTEC	kidney:	n/a
39	chr2:11485413-11485463	LNCaP	prostate:	n/a
40	chr2:11485413-11485463	GM12891	blood:	n/a
41	chr2:11485413-11485463	PANC-1	pancreas:	n/a
42	chr2:11485413-11485463	AoSMC	blood vessel:	n/a
43	chr2:11485413-11485463	HNPCEpiC	eye:	n/a
44	chr2:11485413-11485463	U87	brain:	n/a
45	chr2:11485413-11485463	GM12878	blood:	n/a
46	chr2:11485413-11485463	HUVEC	blood vessel:	n/a
47	chr2:11485413-11485463	MCF10A-Er-Src	breast:	n/a
48	chr2:11485413-11485463	SKMC	muscle:	n/a
49	chr2:11485413-11485463	HEEpiC	esophagus:	n/a
50	chr2:11485413-11485463	NH-A	brain:	n/a

(count:18 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:11446328..11449302-chr2:11482839..11485533,2	MCF-7	breast:
2	chr2:11482372..11487550-chr2:11525654..11531960,9	MCF-7	breast:
3	chr2:11373041..11376680-chr2:11481459..11486793,6	MCF-7	breast:
4	chr2:11481545..11486787-chr2:11491378..11496218,8	MCF-7	breast:
5	chr2:11483291..11485571-chr2:11604286..11606431,2	MCF-7	breast:
6	chr17:27620648..27621777-chr2:11484781..11485516,3	NB4	blood:
7	chr2:11483940..11486207-chr2:11530235..11532034,2	K562	blood:
8	chr2:11292941..11297094-chr2:11480820..11486254,6	MCF-7	breast:
9	chr2:11484521..11487208-chr2:11489833..11492072,2	K562	blood:
10	chr2:11483049..11486978-chr2:11530307..11533471,4	MCF-7	breast:
11	chr2:11462927..11464937-chr2:11485248..11487120,2	K562	blood:
12	chr2:11484922..11486828-chr2:11507256..11509884,2	K562	blood:
13	chr2:10951194..10953015-chr2:11483398..11486312,2	MCF-7	breast:
14	chr2:11484673..11485608-chr6:30584791..30585452,2	Hela-S3	cervix:
15	chr2:11482684..11486384-chr2:11678704..11682899,6	MCF-7	breast:
16	chr2:11485129..11485840-chr2:68479649..68480177,2	Hela-S3	cervix:
17	chr2:11485452..11487445-chr2:11503677..11505301,2	K562	blood:
18	chr2:11484880..11486405-chr2:11487822..11489457,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PQLC3-1	chr2:11485211-11485815	XLOC_001349
2	lnc-PQLC3-1	chr2:11485102-11485815	NONHSAT069160

No data

Variant related genes	Relation type
ROCK2	TF binding region
ROCK2	CpG island
ENSG00000221823	Chromatin interaction
ENSG00000226961	Chromatin interaction
ENSG00000204569	Chromatin interaction
ENSG00000162976	Chromatin interaction
ENSG00000143870	Chromatin interaction
ENSG00000134318	Chromatin interaction
ENSG00000196208	Chromatin interaction
ENSG00000169016	Chromatin interaction
ENSG00000264010	Chromatin interaction
ENSG00000231403	Chromatin interaction
ENSG00000207267	Chromatin interaction
ENSG00000230154	Chromatin interaction
ENSG00000273064	Chromatin interaction
ENSG00000108256	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs10929732	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12467103	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12692437	0.84[AMR][1000 genomes]
rs4669712	0.84[AMR][1000 genomes]
rs4669713	0.84[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526038	chr2:11369078-11489531	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv1010506	chr2:11430965-12057286	Enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
3	nsv535585	chr2:11430965-12057286	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
4	esv3449527	chr2:11483801-11486049	Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10173492	PQLC3	Cis_1M	lymphoblastoid	RTeQTL
rs10173492	ROCK2	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:11480000-11485800	Active TSS	Aorta	Aorta
2	chr2:11481000-11485600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
3	chr2:11481000-11485600	Active TSS	NHLF	lung
4	chr2:11481000-11485800	Active TSS	Ovary	ovary
5	chr2:11481200-11485600	Active TSS	Brain Inferior Temporal Lobe	brain
6	chr2:11481600-11485600	Active TSS	HUES6 Cell Line	embryonic stem cell
7	chr2:11481600-11485600	Active TSS	Brain Germinal Matrix	brain
8	chr2:11481600-11485800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr2:11481800-11485600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr2:11481800-11485600	Active TSS	Fetal Intestine Large	intestine
11	chr2:11481800-11485600	Active TSS	NHDF-Ad	bronchial
12	chr2:11481800-11485800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr2:11481800-11486000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr2:11482000-11485800	Active TSS	ES-I3 Cell Line	embryonic stem cell
15	chr2:11482000-11486000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr2:11482000-11486000	Active TSS	Breast Myoepithelial Primary Cells	Breast
17	chr2:11482200-11485600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr2:11482200-11485600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr2:11482200-11485600	Active TSS	Rectal Smooth Muscle	rectum
20	chr2:11482200-11485800	Active TSS	Fetal Muscle Trunk	muscle
21	chr2:11482200-11485800	Active TSS	Psoas Muscle	Psoas
22	chr2:11482400-11485600	Active TSS	iPS-15b Cell Line	embryonic stem cell
23	chr2:11482400-11485600	Active TSS	iPS-20b Cell Line	embryonic stem cell
24	chr2:11482400-11485600	Active TSS	Brain Anterior Caudate	brain
25	chr2:11482400-11485600	Active TSS	Fetal Intestine Small	intestine
26	chr2:11482400-11485600	Active TSS	Fetal Stomach	stomach
27	chr2:11482400-11485600	Active TSS	Left Ventricle	heart
28	chr2:11482400-11486400	Active TSS	Duodenum Smooth Muscle	Duodenum
29	chr2:11482600-11485600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr2:11482600-11485600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr2:11482600-11485800	Active TSS	HUES64 Cell Line	embryonic stem cell
32	chr2:11482600-11485800	Active TSS	Right Ventricle	heart
33	chr2:11482600-11486000	Active TSS	H1 Cell Line	embryonic stem cell
34	chr2:11482600-11486000	Active TSS	Fetal Kidney	kidney
35	chr2:11482800-11485600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr2:11482800-11485800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr2:11482800-11485800	Active TSS	Colonic Mucosa	Colon
38	chr2:11482800-11485800	Active TSS	Pancreatic Islets	Pancreatic Islet
39	chr2:11483000-11485600	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr2:11483000-11485800	Active TSS	Esophagus	oesophagus
41	chr2:11483000-11486000	Active TSS	HUES48 Cell Line	embryonic stem cell
42	chr2:11483200-11485600	Active TSS	H9 Cell Line	embryonic stem cell
43	chr2:11483200-11485600	Active TSS	Duodenum Mucosa	Duodenum
44	chr2:11483200-11485600	Active TSS	Rectal Mucosa Donor 29	rectum
45	chr2:11483200-11485600	Active TSS	Sigmoid Colon	Sigmoid Colon
46	chr2:11483200-11485600	Active TSS	Small Intestine	intestine
47	chr2:11483200-11485800	Active TSS	Pancreas	Pancrea
48	chr2:11483400-11485600	Active TSS	Brain Substantia Nigra	brain
49	chr2:11483400-11485800	Active TSS	Brain Hippocampus Middle	brain
50	chr2:11483600-11485600	Active TSS	iPS-18 Cell Line	embryonic stem cell

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