Variant report

Variant	rs3748026
Chromosome Location	chr2:113342051-113342052
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:576)
CpG islands
(count:0)
Chromatin interactive
region (count:28)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:576 , 50 per page) page: 1 2 3 4 5 6 7 ... 12

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SPI1	chr2:113341899-113342171	K562	blood:	n/a	n/a
2	BHLHE40	chr2:113341121-113342596	K562	blood:	n/a	n/a
3	SIX5	chr2:113341717-113342283	GM12878	blood:	n/a	n/a
4	CTCF	chr2:113341732-113342410	K562	blood:	n/a	n/a
5	CTCF	chr2:113341940-113342090	AG10803	skin:	n/a	n/a
6	CHD2	chr2:113341713-113342622	K562	blood:	n/a	chr2:113342420-113342430
7	CREB1	chr2:113340867-113342678	HepG2	liver:	n/a	n/a
8	USF2	chr2:113341723-113342430	H1-hESC	embryonic stem cell:	n/a	n/a
9	NFIC	chr2:113341493-113342549	GM12878	blood:	n/a	n/a
10	PML	chr2:113341500-113342565	K562	blood:	n/a	n/a
11	ELF1	chr2:113341452-113342451	K562	blood:	n/a	chr2:113341940-113341953 chr2:113341971-113341984
12	TAF1	chr2:113341389-113342697	ECC-1	luminal epithelium:	n/a	n/a
13	POLR2A	chr2:113341035-113342697	HepG2	liver:	n/a	n/a
14	ELF1	chr2:113341421-113342642	HepG2	liver:	n/a	chr2:113341940-113341953 chr2:113341971-113341984
15	STAT3	chr2:113341883-113342294	MCF10A-Er-Src	breast:	n/a	n/a
16	REST	chr2:113341163-113342631	HL-60	blood:	n/a	n/a
17	CEBPB	chr2:113341780-113342279	IMR90	lung:	n/a	chr2:113341987-113341998
18	CTCF	chr2:113341920-113342070	HBMEC	blood vessel:	n/a	n/a
19	CTCF	chr2:113342044-113342058	MCF-7	breast:	n/a	n/a
20	POLR2A	chr2:113341634-113342706	GM15510	blood:	n/a	n/a
21	POLR2A	chr2:113341428-113342877	Hela-S3	cervix:	n/a	n/a
22	MTA3	chr2:113341029-113342926	GM12878	blood:	n/a	n/a
23	MXI1	chr2:113341045-113342848	HepG2	liver:	n/a	chr2:113342149-113342164
24	TBP	chr2:113341725-113342636	Hela-S3	cervix:	n/a	n/a
25	YY1	chr2:113341310-113342615	GM12878	blood:	n/a	chr2:113342147-113342156 chr2:113342067-113342076
26	POLR2A	chr2:113339455-113342662	K562	blood:	n/a	n/a
27	CTCF	chr2:113341920-113342070	AG09319	gingival:	n/a	n/a
28	ELF1	chr2:113341391-113342619	MCF-7	breast:	n/a	chr2:113341940-113341953 chr2:113341971-113341984
29	JUND	chr2:113341615-113342586	A549	lung:	n/a	n/a
30	MAFK	chr2:113341711-113342404	K562	blood:	n/a	n/a
31	CTCF	chr2:113341920-113342070	K562	blood:	n/a	n/a
32	TCF7L2	chr2:113341570-113342586	HCT-116	colon:	n/a	n/a
33	CTCF	chr2:113341780-113342070	GM12872	blood:	n/a	n/a
34	CREB1	chr2:113341745-113342548	H1-hESC	embryonic stem cell:	n/a	n/a
35	ELF1	chr2:113341580-113342362	A549	lung:	n/a	chr2:113341940-113341953 chr2:113341971-113341984
36	POU2F2	chr2:113341541-113342610	GM12878	blood:	n/a	n/a
37	TAF1	chr2:113341484-113342543	K562	blood:	n/a	n/a
38	SIN3AK20	chr2:113341645-113342597	SK-N-SH	brain:	n/a	n/a
39	POLR2A	chr2:113341022-113342876	U87	brain:	n/a	n/a
40	GABPA	chr2:113341636-113342359	K562	blood:	n/a	n/a
41	ATF1	chr2:113341843-113342332	K562	blood:	n/a	n/a
42	CTCF	chr2:113341920-113342070	GM12869	blood:	n/a	n/a
43	TAF1	chr2:113341635-113342648	PFSK-1	brain:	n/a	n/a
44	SETDB1	chr2:113341549-113342424	K562	blood:	n/a	n/a
45	STAT5A	chr2:113341421-113342584	GM12878	blood:	n/a	n/a
46	SIX5	chr2:113341590-113342762	A549	lung:	n/a	n/a
47	YY1	chr2:113341566-113342322	GM12892	blood:	n/a	chr2:113342147-113342156 chr2:113342067-113342076
48	EGR1	chr2:113341731-113342155	GM12878	blood:	n/a	chr2:113342004-113342018
49	MAX	chr2:113341452-113342712	A549	lung:	n/a	chr2:113342155-113342164 chr2:113342399-113342409
50	CTCF	chr2:113341940-113342090	HMF	breast:	n/a	n/a

No data

(count:28 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr16:56965686..56966536-chr2:113341670..113342477,2	HCT-116	colon:
2	chr1:156697735..156698536-chr2:113341707..113342498,2	Hela-S3	cervix:
3	chr10:75006774..75007379-chr2:113341862..113342735,2	Hela-S3	cervix:
4	chr2:39351098..39351964-chr2:113341975..113342944,2	NB4	blood:
5	chr12:46760893..46761645-chr2:113341924..113342581,2	Hela-S3	cervix:
6	chr2:113335699..113339674-chr2:113340106..113343204,5	K562	blood:
7	chr2:113298954..113302477-chr2:113339455..113343767,5	MCF-7	breast:
8	chr1:24017896..24018591-chr2:113341831..113342469,2	Hela-S3	cervix:
9	chr2:112641083..112643206-chr2:113340920..113342440,2	K562	blood:
10	chr2:113296892..113302637-chr2:113340004..113344909,8	K562	blood:
11	chr2:113340008..113343992-chr2:113483304..113487579,6	K562	blood:
12	chr2:113031869..113034952-chr2:113341167..113343629,3	MCF-7	breast:
13	chr2:113340774..113345524-chr2:113480391..113485957,9	MCF-7	breast:
14	chr1:212208449..212209308-chr2:113342043..113342672,2	Hela-S3	cervix:
15	chr2:113341870..113342554-chr3:182510708..182511419,2	Hela-S3	cervix:
16	chr2:113339547..113343883-chr2:113402286..113405078,6	K562	blood:
17	chr2:113237331..113240789-chr2:113339342..113343125,4	K562	blood:
18	chr2:113340479..113344233-chr2:113401874..113407323,6	MCF-7	breast:
19	chr2:113338959..113342918-chr2:113483353..113487579,5	K562	blood:
20	chr11:10830393..10830898-chr2:113341610..113342362,2	Hela-S3	cervix:
21	chr2:113339547..113342143-chr2:113401632..113406213,6	K562	blood:
22	chr2:113298569..113302646-chr2:113339335..113343133,7	K562	blood:
23	chr2:113340437..113343949-chr2:113401268..113406617,9	MCF-7	breast:
24	chr2:113298759..113301838-chr2:113339526..113343252,4	MCF-7	breast:
25	chr2:113341475..113342295-chr7:108166193..108166767,2	Hela-S3	cervix:
26	chr2:113235824..113243298-chr2:113338675..113344022,16	MCF-7	breast:
27	chr2:113307316..113310204-chr2:113340273..113342615,2	MCF-7	breast:
28	chr2:113010958..113014005-chr2:113340303..113342675,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000207383	TF binding region
ENSG00000243389	TF binding region
CHCHD5	TF binding region
ENSG00000236756	Chromatin interaction
ENSG00000144130	Chromatin interaction
ENSG00000110321	Chromatin interaction
ENSG00000143476	Chromatin interaction
ENSG00000240063	Chromatin interaction
ENSG00000125630	Chromatin interaction
ENSG00000114999	Chromatin interaction
ENSG00000246308	Chromatin interaction
ENSG00000142676	Chromatin interaction
ENSG00000188177	Chromatin interaction
ENSG00000144136	Chromatin interaction
ENSG00000134294	Chromatin interaction
ENSG00000153107	Chromatin interaction
ENSG00000237753	Chromatin interaction
ENSG00000144161	Chromatin interaction
ENSG00000143303	Chromatin interaction
ENSG00000143319	Chromatin interaction
ENSG00000143493	Chromatin interaction
ENSG00000135241	Chromatin interaction
ENSG00000115904	Chromatin interaction
ENSG00000051108	Chromatin interaction
ENSG00000058063	Chromatin interaction
ENSG00000207383	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10169290	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10169344	1.00[CEU][hapmap];0.88[GIH][hapmap];0.94[MEX][hapmap];0.91[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10183849	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10205187	0.89[CEU][hapmap];0.88[GIH][hapmap];0.84[MEX][hapmap];0.91[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13395691	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[GIH][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.91[TSI][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13395779	1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.91[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13412193	1.00[CEU][hapmap];0.88[GIH][hapmap];0.84[MEX][hapmap];0.83[TSI][hapmap]
rs13413001	0.82[AMR][1000 genomes]
rs1583616	0.88[CEU][hapmap]
rs2241804	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3789724	1.00[CEU][hapmap];0.88[GIH][hapmap];0.84[MEX][hapmap];0.83[TSI][hapmap]
rs3961914	0.84[EUR][1000 genomes]
rs57339041	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][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	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7576952	0.88[CEU][hapmap]

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
rs3748026	POLR1B	cis	Artery Tibial	GTEx
rs3748026	POLR1B	cis	Stomach	GTEx
rs3748026	POLR1B	cis	Whole Blood	GTEx
rs3748026	POLR1B	cis	Adipose Subcutaneous	GTEx
rs3748026	POLR1B	cis	Thyroid	GTEx
rs3748026	POLR1B	cis	Esophagus Muscularis	GTEx
rs3748026	POLR1B	cis	Nerve Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113340400-113342400	Active TSS	Pancreas	Pancrea
2	chr2:113340800-113342600	Active TSS	Fetal Brain Male	brain
3	chr2:113340800-113342800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr2:113340800-113342800	Active TSS	HUES6 Cell Line	embryonic stem cell
5	chr2:113340800-113343000	Active TSS	HUES64 Cell Line	embryonic stem cell
6	chr2:113341000-113342400	Active TSS	Fetal Lung	lung
7	chr2:113341000-113342400	Active TSS	Fetal Muscle Trunk	muscle
8	chr2:113341000-113342400	Active TSS	HSMMtube	muscle
9	chr2:113341000-113342600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr2:113341000-113342600	Active TSS	iPS-20b Cell Line	embryonic stem cell
11	chr2:113341000-113342600	Active TSS	Psoas Muscle	Psoas
12	chr2:113341000-113342800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
13	chr2:113341000-113342800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr2:113341000-113343000	Active TSS	ES-I3 Cell Line	embryonic stem cell
15	chr2:113341000-113343400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr2:113341200-113342600	Active TSS	iPS-15b Cell Line	embryonic stem cell
17	chr2:113341200-113342600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr2:113341200-113342600	Active TSS	Brain Inferior Temporal Lobe	brain
19	chr2:113341200-113342600	Active TSS	Duodenum Smooth Muscle	Duodenum
20	chr2:113341200-113342600	Active TSS	Left Ventricle	heart
21	chr2:113341200-113342600	Active TSS	Lung	lung
22	chr2:113341200-113342600	Active TSS	Right Ventricle	heart
23	chr2:113341200-113342800	Active TSS	iPS-18 Cell Line	embryonic stem cell
24	chr2:113341200-113342800	Flanking Active TSS	Primary hematopoietic stem cells	blood
25	chr2:113341200-113342800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr2:113341200-113343000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr2:113341200-113343000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
28	chr2:113341200-113343200	Active TSS	HUES48 Cell Line	embryonic stem cell
29	chr2:113341200-113343400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
30	chr2:113341400-113342200	Active TSS	Brain Angular Gyrus	brain
31	chr2:113341400-113342400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr2:113341400-113342400	Active TSS	Brain Substantia Nigra	brain
33	chr2:113341400-113342400	Active TSS	Fetal Adrenal Gland	Adrenal Gland
34	chr2:113341400-113342400	Active TSS	Stomach Mucosa	stomach
35	chr2:113341400-113342400	Active TSS	K562	blood
36	chr2:113341400-113342600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr2:113341400-113342600	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr2:113341400-113342600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr2:113341400-113342600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr2:113341400-113342600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr2:113341400-113342600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr2:113341400-113342600	Active TSS	Breast Myoepithelial Primary Cells	Breast
43	chr2:113341400-113342600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr2:113341400-113342600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr2:113341400-113342600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr2:113341400-113342600	Active TSS	Brain Anterior Caudate	brain
47	chr2:113341400-113342600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
48	chr2:113341400-113342600	Active TSS	Fetal Intestine Large	intestine
49	chr2:113341400-113342600	Active TSS	Fetal Intestine Small	intestine
50	chr2:113341400-113342600	Active TSS	Fetal Kidney	kidney

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