Variant report

Variant	rs2241804
Chromosome Location	chr2:113300283-113300284
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:375)
CpG islands
(count:61)
Chromatin interactive
region (count:24)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:375 , 50 per page) page: 1 2 3 4 5 6 7 8

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SREBP1	chr2:113297940-113301472	GM12878	blood:	n/a	n/a
2	MAZ	chr2:113299068-113300291	K562	blood:	n/a	n/a
3	MAX	chr2:113299240-113300573	SK-N-SH	brain:	n/a	chr2:113300065-113300075
4	GABPA	chr2:113299063-113300682	A549	lung:	n/a	n/a
5	POLR2A	chr2:113299265-113300479	Hela-S3	cervix:	n/a	n/a
6	STAT5A	chr2:113298900-113300858	GM12878	blood:	n/a	chr2:113299826-113299838 chr2:113299452-113299464 chr2:113300733-113300742 chr2:113300732-113300741 chr2:113299913-113299924
7	REST	chr2:113299318-113300307	SK-N-SH	brain:	n/a	chr2:113299761-113299771
8	RCOR1	chr2:113299278-113300365	HepG2	liver:	n/a	n/a
9	BRCA1	chr2:113299404-113301022	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr2:113299005-113300531	GM12892	blood:	n/a	n/a
11	POLR2A	chr2:113299228-113300363	K562	blood:	n/a	n/a
12	POLR2A	chr2:113299009-113300573	GM12891	blood:	n/a	n/a
13	POLR2A	chr2:113298829-113300455	GM12878	blood:	n/a	n/a
14	ZNF384	chr2:113299915-113300386	K562	blood:	n/a	n/a
15	EP300	chr2:113299413-113300371	A549	lung:	n/a	n/a
16	POLR2A	chr2:113299223-113300415	MCF-7	breast:	n/a	n/a
17	ZEB1	chr2:113299269-113300292	GM12878	blood:	n/a	chr2:113300242-113300254 chr2:113299660-113299671
18	USF1	chr2:113299369-113300324	A549	lung:	n/a	n/a
19	USF1	chr2:113299343-113300290	HepG2	liver:	n/a	n/a
20	ATF2	chr2:113299693-113300320	H1-hESC	embryonic stem cell:	n/a	n/a
21	POLR2A	chr2:113298891-113300511	GM12878	blood:	n/a	n/a
22	MYC	chr2:113299840-113300389	MCF-7	breast:	n/a	chr2:113300065-113300075
23	YY1	chr2:113299256-113300483	GM12878	blood:	n/a	chr2:113299406-113299417
24	ZNF143	chr2:113299271-113300357	H1-hESC	embryonic stem cell:	n/a	chr2:113299956-113299974 chr2:113299956-113299965 chr2:113299960-113299979 chr2:113299958-113299967
25	CBX3	chr2:113298818-113300636	K562	blood:	n/a	n/a
26	USF1	chr2:113299129-113300478	HCT-116	colon:	n/a	n/a
27	MYC	chr2:113299443-113300590	K562	blood:	n/a	chr2:113300065-113300075
28	ZBTB33	chr2:113299651-113300328	GM12878	blood:	n/a	n/a
29	POLR2A	chr2:113299231-113300570	H1-neurons	neurons:	n/a	n/a
30	TBL1XR1	chr2:113299174-113300313	GM12878	blood:	n/a	n/a
31	GABPA	chr2:113299216-113300678	MCF-7	breast:	n/a	n/a
32	POLR2A	chr2:113299154-113300335	HCT-116	colon:	n/a	n/a
33	TCF3	chr2:113299659-113300409	GM12878	blood:	n/a	n/a
34	SMC3	chr2:113300170-113300288	GM12878	blood:	n/a	n/a
35	POLR2A	chr2:113298847-113300412	GM18526	blood:	n/a	n/a
36	RFX5	chr2:113299303-113300466	Hela-S3	cervix:	n/a	chr2:113299724-113299733
37	POLR2A	chr2:113298860-113300532	K562	blood:	n/a	n/a
38	SIN3AK20	chr2:113299852-113300288	PFSK-1	brain:	n/a	n/a
39	BRCA1	chr2:113299475-113300346	H1-hESC	embryonic stem cell:	n/a	n/a
40	POLR2A	chr2:113299123-113300517	PFSK-1	brain:	n/a	n/a
41	USF1	chr2:113299447-113300357	H1-hESC	embryonic stem cell:	n/a	n/a
42	YY1	chr2:113299457-113300470	H1-hESC	embryonic stem cell:	n/a	n/a
43	RELA	chr2:113298896-113300502	GM12891	blood:	n/a	n/a
44	ZBTB33	chr2:113299723-113300334	HCT-116	colon:	n/a	n/a
45	SIN3AK20	chr2:113299874-113300354	K562	blood:	n/a	n/a
46	POLR2A	chr2:113299181-113300517	MCF-7	breast:	n/a	n/a
47	POLR2A	chr2:113299082-113300569	GM12878	blood:	n/a	n/a
48	IRF1	chr2:113298730-113300291	K562	blood:	n/a	chr2:113299911-113299924 chr2:113299913-113299924 chr2:113299912-113299926 chr2:113299911-113299924 chr2:113299910-113299924 chr2:113299911-113299924 chr2:113299911-113299925 chr2:113299912-113299925 chr2:113299911-113299924 chr2:113299915-113299925 chr2:113299914-113299925 chr2:113299912-113299926 chr2:113299913-113299927
49	POLR2A	chr2:113299252-113300401	A549	lung:	n/a	n/a
50	YY1	chr2:113299308-113300334	ECC-1	luminal epithelium:	n/a	chr2:113299406-113299417

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr2:113300283-113300333	NH-A	brain:	n/a
2	chr2:113300283-113300333	HMEC	breast:	n/a
3	chr2:113300283-113300333	PANC-1	pancreas:	n/a
4	chr2:113300283-113300333	HEK293	kidney:	embryo
5	chr2:113300283-113300333	MCF-7	breast:	n/a
6	chr2:113300283-113300333	HPAEpiC	pulmonary alveolar:	n/a
7	chr2:113300283-113300333	SK-N-SH	brain:	n/a
8	chr2:113300283-113300333	HIPEpiC	eye:	n/a
9	chr2:113300283-113300333	HCF	heart:	n/a
10	chr2:113300283-113300333	HUVEC	blood vessel:	n/a
11	chr2:113300283-113300333	HNPCEpiC	eye:	n/a
12	chr2:113300283-113300333	K562	blood:	n/a
13	chr2:113300283-113300333	H1-hESC	embryonic stem cell:	embryo
14	chr2:113300283-113300333	HRCEpiC	kidney:	n/a
15	chr2:113300283-113300333	HCM	heart:	n/a
16	chr2:113300283-113300333	BJ	skin:	n/a
17	chr2:113300283-113300333	GM06990	blood:	n/a
18	chr2:113300283-113300333	SK-N-MC	brain:	n/a
19	chr2:113300283-113300333	AG04450	lung:	fetal
20	chr2:113300283-113300333	ECC-1	luminal epithelium:	n/a
21	chr2:113300283-113300333	HRE	kidney:	n/a
22	chr2:113300283-113300333	GM12878	blood:	n/a
23	chr2:113300283-113300333	MCF10A-Er-Src	breast:	n/a
24	chr2:113300283-113300333	Caco-2	colon:	n/a
25	chr2:113300283-113300333	PrEC	prostate:	n/a
26	chr2:113300283-113300333	HL-60	blood:	n/a
27	chr2:113300283-113300333	Jurkat	blood:	n/a
28	chr2:113300283-113300333	RPTEC	kidney:	n/a
29	chr2:113300283-113300333	T-47D	breast:	n/a
30	chr2:113300283-113300333	HEEpiC	esophagus:	n/a
31	chr2:113300283-113300333	SAEC	small airway:	n/a
32	chr2:113300283-113300333	NHBE	bronchial:	n/a
33	chr2:113300283-113300333	NB4	blood:	n/a
34	chr2:113300283-113300333	PFSK-1	brain:	n/a
35	chr2:113300283-113300333	ovcar-3	ovarian:	n/a
36	chr2:113300283-113300333	ProgFib	skin:	n/a
37	chr2:113300283-113300333	BE2_C	brain:	n/a
38	chr2:113300283-113300333	HRPEpiC	eye:	n/a
39	chr2:113300283-113300333	GM12892	blood:	n/a
40	chr2:113300283-113300333	IMR90	lung:	fetal
41	chr2:113300283-113300333	GM12891	blood:	n/a
42	chr2:113300283-113300333	LNCaP	prostate:	n/a
43	chr2:113300283-113300333	HepG2	liver:	n/a
44	chr2:113300283-113300333	U87	brain:	n/a
45	chr2:113300283-113300333	NHDF-neo	bronchial:	n/a
46	chr2:113300283-113300333	A549	lung:	n/a
47	chr2:113300283-113300333	Hela-S3	cervix:	n/a
48	chr2:113300283-113300333	HCT-116	colon:	n/a
49	chr2:113300283-113300333	AoSMC	blood vessel:	n/a
50	chr2:113300283-113300333	Hepatocyte	liver:	n/a

(count:24 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:113300113..113302309-chr2:113304266..113305973,2	MCF-7	breast:
2	chr2:113297896..113300759-chr2:113319163..113321961,2	K562	blood:
3	chr2:113298569..113302646-chr2:113339335..113343133,7	K562	blood:
4	chr2:113296892..113302637-chr2:113340004..113344909,8	K562	blood:
5	chr2:113298759..113301838-chr2:113339526..113343252,4	MCF-7	breast:
6	chr12:52584189..52586153-chr2:113298687..113301459,2	MCF-7	breast:
7	chr2:113298665..113301106-chr2:113481233..113484131,2	MCF-7	breast:
8	chr2:113297047..113302352-chr2:113483159..113487384,5	K562	blood:
9	chr2:113299867..113302656-chr2:113306781..113308489,3	MCF-7	breast:
10	chr2:113299816..113300466-chr8:29207781..29208419,2	HCT-116	colon:
11	chr2:113032895..113034868-chr2:113298043..113301369,3	K562	blood:
12	chr2:112640408..112642506-chr2:113299856..113302341,2	K562	blood:
13	chr2:113299836..113301714-chr2:113487045..113489440,2	MCF-7	breast:
14	chr2:113298945..113301583-chr2:113309336..113312263,4	MCF-7	breast:
15	chr2:112811580..112813458-chr2:113297904..113301248,3	K562	blood:
16	chr2:113235916..113241390-chr2:113298151..113302275,12	MCF-7	breast:
17	chr2:113277911..113280966-chr2:113298764..113301565,3	MCF-7	breast:
18	chr2:112811382..112813355-chr2:113297904..113301187,3	K562	blood:
19	chr2:113012601..113015047-chr2:113298969..113301494,2	K562	blood:
20	chr2:113238238..113241697-chr2:113298157..113301092,6	K562	blood:
21	chr2:113031538..113036695-chr2:113297613..113301921,6	K562	blood:
22	chr2:113298954..113302477-chr2:113339455..113343767,5	MCF-7	breast:
23	chr2:113238895..113243312-chr2:113297571..113302127,8	K562	blood:
24	chr2:113235572..113240260-chr2:113300212..113305167,6	MCF-7	breast:

No data

Variant related genes	Relation type
POLR1B	TF binding region
POLR1B	CpG island
ENSG00000125611	Chromatin interaction
ENSG00000153214	Chromatin interaction
ENSG00000114999	Chromatin interaction
ENSG00000167767	Chromatin interaction
ENSG00000120875	Chromatin interaction
ENSG00000144161	Chromatin interaction
ENSG00000153107	Chromatin interaction
ENSG00000188177	Chromatin interaction
ENSG00000125630	Chromatin interaction
ENSG00000144130	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10169290	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10169344	1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[JPT][hapmap];0.87[YRI][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10183849	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10200067	0.92[ASN][1000 genomes]
rs10205187	0.82[CEU][hapmap];0.88[CHB][hapmap];0.92[JPT][hapmap];0.87[YRI][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13395691	1.00[CEU][hapmap];0.88[CHB][hapmap];0.92[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13395779	1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13412193	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13413001	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13424021	0.98[ASN][1000 genomes]
rs1583616	0.94[CHB][hapmap];0.92[JPT][hapmap];0.81[YRI][hapmap];0.98[ASN][1000 genomes]
rs3748026	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3789724	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3961914	0.93[ASN][1000 genomes]
rs57339041	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs59033131	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60489148	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60518507	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61669219	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62158580	0.92[ASN][1000 genomes]
rs62158582	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62158584	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62158585	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62158586	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62158591	0.95[ASN][1000 genomes]
rs62158643	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62158644	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7565714	0.83[CHB][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs7565827	0.87[ASN][1000 genomes]
rs9308671	0.87[ASN][1000 genomes]
rs9308672	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9808491	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[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	nsv949573	chr2:112986955-113320975	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2241804	POLR1B	cis	Esophagus Muscularis	GTEx
rs2241804	POLR1B	cis	Nerve Tibial	GTEx
rs2241804	POLR1B	cis	Thyroid	GTEx
rs2241804	POLR1B	cis	Artery Tibial	GTEx
rs2241804	POLR1B	cis	Adipose Subcutaneous	GTEx
rs2241804	POLR1B	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113298600-113301200	Active TSS	K562	blood
2	chr2:113298600-113301600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr2:113298600-113303600	Active TSS	GM12878-XiMat	blood
4	chr2:113298800-113300600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
5	chr2:113298800-113300800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr2:113298800-113300800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr2:113298800-113300800	Active TSS	Aorta	Aorta
8	chr2:113298800-113301200	Active TSS	iPS-18 Cell Line	embryonic stem cell
9	chr2:113298800-113301600	Active TSS	HUES64 Cell Line	embryonic stem cell
10	chr2:113298800-113301600	Active TSS	iPS-20b Cell Line	embryonic stem cell
11	chr2:113298800-113301600	Active TSS	Pancreatic Islets	Pancreatic Islet
12	chr2:113299000-113300400	Active TSS	Right Ventricle	heart
13	chr2:113299000-113300600	Active TSS	Colon Smooth Muscle	Colon
14	chr2:113299000-113300800	Active TSS	H1 Cell Line	embryonic stem cell
15	chr2:113299000-113300800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr2:113299000-113300800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr2:113299000-113300800	Active TSS	Colonic Mucosa	Colon
18	chr2:113299000-113300800	Active TSS	Fetal Kidney	kidney
19	chr2:113299000-113300800	Active TSS	Right Atrium	heart
20	chr2:113299000-113300800	Active TSS	NHLF	lung
21	chr2:113299000-113301200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
22	chr2:113299000-113301200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr2:113299000-113301200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
24	chr2:113299000-113301600	Active TSS	ES-I3 Cell Line	embryonic stem cell
25	chr2:113299000-113301600	Active TSS	H9 Cell Line	embryonic stem cell
26	chr2:113299000-113301600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr2:113299000-113301600	Active TSS	HUES48 Cell Line	embryonic stem cell
28	chr2:113299000-113301600	Active TSS	HUES6 Cell Line	embryonic stem cell
29	chr2:113299000-113301600	Active TSS	iPS-15b Cell Line	embryonic stem cell
30	chr2:113299200-113300400	Active TSS	Brain Inferior Temporal Lobe	brain
31	chr2:113299200-113300400	Active TSS	Brain Substantia Nigra	brain
32	chr2:113299200-113300400	Active TSS	Stomach Smooth Muscle	stomach
33	chr2:113299200-113300400	Active TSS	Osteobl	bone
34	chr2:113299200-113300600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr2:113299200-113300600	Active TSS	Brain Angular Gyrus	brain
36	chr2:113299200-113300600	Active TSS	Brain Cingulate Gyrus	brain
37	chr2:113299200-113300600	Active TSS	Duodenum Smooth Muscle	Duodenum
38	chr2:113299200-113300600	Active TSS	Fetal Stomach	stomach
39	chr2:113299200-113300800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr2:113299200-113300800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr2:113299200-113300800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr2:113299200-113300800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
43	chr2:113299200-113300800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr2:113299200-113300800	Active TSS	Brain Anterior Caudate	brain
45	chr2:113299200-113300800	Active TSS	Esophagus	oesophagus
46	chr2:113299200-113300800	Active TSS	Fetal Brain Male	brain
47	chr2:113299200-113300800	Active TSS	Gastric	stomach
48	chr2:113299200-113300800	Active TSS	Left Ventricle	heart
49	chr2:113299200-113300800	Active TSS	Lung	lung
50	chr2:113299200-113300800	Active TSS	Ovary	ovary

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