Variant report

Variant	rs57339041
Chromosome Location	chr2:113340106-113340107
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:89)
CpG islands
(count:0)
Chromatin interactive
region (count:20)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:89 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr2:113340024-113340162	GM12878	blood:	n/a	n/a
2	RAD21	chr2:113339834-113340224	H1-hESC	embryonic stem cell:	n/a	n/a
3	CTCF	chr2:113339904-113340141	K562	blood:	n/a	n/a
4	POLR2A	chr2:113339807-113340761	MCF10A-Er-Src	breast:	n/a	n/a
5	POLR2A	chr2:113339455-113342662	K562	blood:	n/a	n/a
6	RAD21	chr2:113339694-113340782	SK-N-SH	brain:	n/a	n/a
7	CTCF	chr2:113339921-113340168	Lung_OC	lung:	n/a	n/a
8	CTCF	chr2:113339856-113340149	K562	blood:	n/a	n/a
9	SMC3	chr2:113339886-113340170	GM12878	blood:	n/a	n/a
10	RAD21	chr2:113339697-113340279	HCT-116	colon:	n/a	n/a
11	RAD21	chr2:113339854-113340126	GM12878	blood:	n/a	n/a
12	CTCF	chr2:113339960-113340110	HA-sp	spinal cord:	n/a	n/a
13	CTCF	chr2:113339831-113340198	K562	blood:	n/a	n/a
14	CTCF	chr2:113339849-113340118	SK-N-SH_RA	brain:	n/a	n/a
15	CTCF	chr2:113339833-113340163	A549	lung:	n/a	n/a
16	CTCF	chr2:113339960-113340110	RPTEC	kidney:	n/a	n/a
17	CTCF	chr2:113339960-113340110	MCF-7	breast:	n/a	n/a
18	RAD21	chr2:113339867-113340194	K562	blood:	n/a	n/a
19	CTCF	chr2:113339980-113340130	HRE	kidney:	n/a	n/a
20	RAD21	chr2:113339895-113340154	HepG2	liver:	n/a	n/a
21	PAX5	chr2:113340031-113340222	GM12878	blood:	n/a	n/a
22	POLR2A	chr2:113339883-113340267	K562	blood:	n/a	n/a
23	RAD21	chr2:113339873-113340188	A549	lung:	n/a	n/a
24	RAD21	chr2:113339785-113340125	A549	lung:	n/a	n/a
25	CTCF	chr2:113339934-113340113	LNCaP	prostate:	n/a	n/a
26	RAD21	chr2:113339723-113340303	MCF-7	breast:	n/a	n/a
27	CTCF	chr2:113339916-113340107	LNCaP	prostate:	n/a	n/a
28	RAD21	chr2:113339862-113340201	Hela-S3	cervix:	n/a	n/a
29	POLR2A	chr2:113340060-113340574	HepG2	liver:	n/a	n/a
30	CTCF	chr2:113339613-113340583	A549	lung:	n/a	n/a
31	RAD21	chr2:113339856-113340203	IMR90	lung:	n/a	n/a
32	RAD21	chr2:113339748-113340296	A549	lung:	n/a	n/a
33	RAD21	chr2:113339854-113340122	GM12878	blood:	n/a	n/a
34	MAX	chr2:113339904-113340163	NB4	blood:	n/a	n/a
35	PAX5	chr2:113340001-113340309	GM12878	blood:	n/a	n/a
36	SMC3	chr2:113339866-113340172	Hela-S3	cervix:	n/a	n/a
37	RAD21	chr2:113339787-113340247	MCF-7	breast:	n/a	n/a
38	MXI1	chr2:113339795-113340112	GM12878	blood:	n/a	n/a
39	CTCF	chr2:113339960-113340110	HCT-116	colon:	n/a	n/a
40	RAD21	chr2:113339942-113340106	K562	blood:	n/a	n/a
41	CTCF	chr2:113339924-113340110	Pancreas_OC	pancreas:	n/a	n/a
42	ZNF384	chr2:113339829-113340406	GM12878	blood:	n/a	n/a
43	MXI1	chr2:113339623-113340430	SK-N-SH	brain:	n/a	n/a
44	CTCF	chr2:113339877-113340201	H1-hESC	embryonic stem cell:	n/a	n/a
45	RAD21	chr2:113339815-113340241	HepG2	liver:	n/a	n/a
46	CTCF	chr2:113339940-113340113	A549	lung:	n/a	n/a
47	CTCF	chr2:113339676-113340796	SK-N-SH	brain:	n/a	n/a
48	CTCF	chr2:113339960-113340110	NHLF	lung:	n/a	n/a
49	PAX5	chr2:113339959-113340301	GM12878	blood:	n/a	n/a
50	CTCF	chr2:113339875-113340142	HepG2	liver:	n/a	n/a

No data

(count:20 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:113339829..113340451-chr2:113357337..113357890,2	MCF-7	breast:
2	chr2:113340042..113340549-chr2:113483924..113484572,2	K562	blood:
3	chr2:112655191..112655972-chr2:113339541..113340327,2	K562	blood:
4	chr2:113238340..113238888-chr2:113339539..113340118,3	MCF-7	breast:
5	chr2:113335699..113339674-chr2:113340106..113343204,5	K562	blood:
6	chr2:113298954..113302477-chr2:113339455..113343767,5	MCF-7	breast:
7	chr2:113296892..113302637-chr2:113340004..113344909,8	K562	blood:
8	chr2:113340008..113343992-chr2:113483304..113487579,6	K562	blood:
9	chr2:113339547..113343883-chr2:113402286..113405078,6	K562	blood:
10	chr2:113237331..113240789-chr2:113339342..113343125,4	K562	blood:
11	chr2:113338959..113342918-chr2:113483353..113487579,5	K562	blood:
12	chr2:113339547..113342143-chr2:113401632..113406213,6	K562	blood:
13	chr2:113238262..113239491-chr2:113339473..113340596,7	K562	blood:
14	chr15:52311460..52312972-chr2:113339826..113341525,2	MCF-7	breast:
15	chr2:113238986..113241764-chr2:113336898..113340191,3	MCF-7	breast:
16	chr2:113298569..113302646-chr2:113339335..113343133,7	K562	blood:
17	chr2:113339955..113341936-chr2:113481777..113484601,3	MCF-7	breast:
18	chr2:113302730..113305146-chr2:113339487..113341558,2	K562	blood:
19	chr2:113298759..113301838-chr2:113339526..113343252,4	MCF-7	breast:
20	chr2:113235824..113243298-chr2:113338675..113344022,16	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RGPD8-5	chr2:113339416-113342035	NONHSAT073700

No data

Variant related genes	Relation type
ENSG00000207383	TF binding region
CHCHD5	TF binding region
ENSG00000069956	Chromatin interaction
ENSG00000144136	Chromatin interaction
ENSG00000207383	Chromatin interaction
ENSG00000144130	Chromatin interaction
ENSG00000125630	Chromatin interaction
ENSG00000114999	Chromatin interaction
ENSG00000237753	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10169290	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10169344	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10183849	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10205187	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13395691	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13395779	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13413001	0.82[AMR][1000 genomes]
rs2241804	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3748026	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3961914	0.84[EUR][1000 genomes]
rs62158582	0.82[AMR][1000 genomes]
rs62158584	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs62158643	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62158644	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][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	nsv874877	chr2:113287964-113382054	Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
2	nsv458997	chr2:113313794-113431092	Flanking Active TSS Strong transcription Weak transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
3	nsv582708	chr2:113313794-113431092	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs57339041	POLR1B	cis	Whole Blood	GTEx
rs57339041	POLR1B	cis	Artery Tibial	GTEx
rs57339041	POLR1B	cis	Thyroid	GTEx
rs57339041	POLR1B	cis	Stomach	GTEx
rs57339041	POLR1B	cis	Nerve Tibial	GTEx
rs57339041	POLR1B	cis	Esophagus Muscularis	GTEx
rs57339041	POLR1B	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113301200-113340200	Weak transcription	Right Atrium	heart
2	chr2:113301200-113341000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr2:113326400-113340200	Weak transcription	Stomach Mucosa	stomach
4	chr2:113326600-113341000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr2:113331400-113340800	Weak transcription	Fetal Brain Male	brain
6	chr2:113331400-113341400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr2:113332200-113341600	Weak transcription	Small Intestine	intestine
8	chr2:113333000-113340800	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr2:113333000-113341000	Weak transcription	Rectal Smooth Muscle	rectum
10	chr2:113333200-113341000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr2:113333200-113341000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr2:113333200-113341000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr2:113333200-113341000	Weak transcription	Fetal Kidney	kidney
14	chr2:113333200-113341200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr2:113333200-113341200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr2:113333200-113341200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr2:113333200-113341200	Weak transcription	Lung	lung
18	chr2:113333400-113340200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr2:113333400-113340800	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr2:113333400-113341000	Weak transcription	Spleen	Spleen
21	chr2:113333600-113341000	Weak transcription	Gastric	stomach
22	chr2:113333600-113341400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr2:113333800-113340200	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr2:113333800-113340800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr2:113333800-113341000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr2:113333800-113341000	Weak transcription	Right Ventricle	heart
27	chr2:113334000-113340200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr2:113334000-113340200	Weak transcription	Adipose Nuclei	Adipose
29	chr2:113334000-113340200	Weak transcription	Colon Smooth Muscle	Colon
30	chr2:113334000-113340800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr2:113334000-113341000	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr2:113334200-113340200	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr2:113334200-113340400	Weak transcription	Primary neutrophils fromperipheralblood	blood
34	chr2:113334200-113340800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr2:113334200-113340800	Weak transcription	Primary hematopoietic stem cells	blood
36	chr2:113334200-113340800	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr2:113334200-113340800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr2:113334200-113341000	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr2:113334200-113341200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr2:113334200-113341200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr2:113334400-113340200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr2:113334400-113340200	Weak transcription	Esophagus	oesophagus
43	chr2:113334400-113340200	Weak transcription	Fetal Intestine Large	intestine
44	chr2:113334400-113340200	Weak transcription	Left Ventricle	heart
45	chr2:113334400-113340200	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr2:113334400-113340600	Weak transcription	Brain Angular Gyrus	brain
47	chr2:113334400-113340600	Weak transcription	Psoas Muscle	Psoas
48	chr2:113334400-113340800	Weak transcription	HUES64 Cell Line	embryonic stem cell
49	chr2:113334400-113340800	Weak transcription	Brain Germinal Matrix	brain
50	chr2:113334400-113340800	Weak transcription	Stomach Smooth Muscle	stomach

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