Variant report

Variant	rs3741530
Chromosome Location	chr12:123469647-123469648
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:56)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:56 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MYC	chr12:123469616-123469792	K562	blood:	n/a	n/a
2	POLR2A	chr12:123469593-123470171	ProgFib	skin:	n/a	n/a
3	POLR2A	chr12:123469184-123470163	GM12878	blood:	n/a	n/a
4	POLR2A	chr12:123468573-123469692	GM19193	blood:	n/a	n/a
5	POLR2A	chr12:123467481-123470043	PANC-1	pancreas:	n/a	n/a
6	POLR2A	chr12:123468278-123469717	U87	brain:	n/a	n/a
7	POLR2A	chr12:123462020-123470019	SK-N-MC	brain:	n/a	n/a
8	POLR2A	chr12:123466333-123470624	K562	blood:	n/a	n/a
9	POLR2A	chr12:123468580-123470167	MCF10A-Er-Src	breast:	n/a	n/a
10	POLR2A	chr12:123467600-123469651	HepG2	liver:	n/a	n/a
11	POLR2A	chr12:123468866-123469821	SK-N-SH	brain:	n/a	n/a
12	POLR2A	chr12:123469538-123469680	A549	lung:	n/a	n/a
13	POLR2A	chr12:123468420-123470561	GM12878	blood:	n/a	n/a
14	MAFK	chr12:123469329-123469647	HepG2	liver:	n/a	n/a
15	ZNF384	chr12:123469396-123469931	K562	blood:	n/a	n/a
16	MAX	chr12:123468677-123469866	HepG2	liver:	n/a	n/a
17	POLR2A	chr12:123469118-123469934	GM12891	blood:	n/a	n/a
18	POLR2A	chr12:123466896-123469748	PFSK-1	brain:	n/a	n/a
19	POLR2A	chr12:123467205-123469730	HL-60	blood:	n/a	n/a
20	POLR2A	chr12:123468750-123469692	HepG2	liver:	n/a	n/a
21	POLR2A	chr12:123468561-123469904	HUVEC	blood vessel:	n/a	n/a
22	POLR2A	chr12:123469479-123470027	HCT-116	colon:	n/a	n/a
23	POLR2A	chr12:123463863-123469964	PFSK-1	brain:	n/a	n/a
24	MAX	chr12:123468513-123470083	HepG2	liver:	n/a	n/a
25	MYBL2	chr12:123468564-123469900	HepG2	liver:	n/a	n/a
26	POLR2A	chr12:123467838-123469667	HUVEC	blood vessel:	n/a	n/a
27	POLR2A	chr12:123468021-123470507	MCF10A-Er-Src	breast:	n/a	n/a
28	POLR2A	chr12:123466981-123470521	GM12878	blood:	n/a	n/a
29	EGR1	chr12:123469605-123469940	K562	blood:	n/a	chr12:123469829-123469843 chr12:123469802-123469816
30	EGR1	chr12:123469623-123469947	K562	blood:	n/a	chr12:123469829-123469843 chr12:123469802-123469816
31	POLR2A	chr12:123469543-123469685	A549	lung:	n/a	n/a
32	POLR2A	chr12:123468510-123469723	GM12892	blood:	n/a	n/a
33	POLR2A	chr12:123468091-123469679	HUVEC	blood vessel:	n/a	n/a
34	MYBL2	chr12:123468756-123469647	HepG2	liver:	n/a	n/a
35	POLR2A	chr12:123468284-123469711	U87	brain:	n/a	n/a
36	NFIC	chr12:123469007-123469789	HepG2	liver:	n/a	n/a
37	POLR2A	chr12:123468458-123470269	GM12891	blood:	n/a	n/a
38	TEAD4	chr12:123469600-123469948	K562	blood:	n/a	n/a
39	RCOR1	chr12:123469614-123469932	K562	blood:	n/a	n/a
40	POLR2A	chr12:123468483-123469865	GM12892	blood:	n/a	n/a
41	MTA3	chr12:123468984-123470384	GM12878	blood:	n/a	n/a
42	MBD4	chr12:123468850-123469748	HepG2	liver:	n/a	n/a
43	POLR2A	chr12:123469596-123469721	H1-hESC	embryonic stem cell:	n/a	n/a
44	POLR2A	chr12:123467406-123470505	HepG2	liver:	n/a	n/a
45	POLR2A	chr12:123468441-123469783	HUVEC	blood vessel:	n/a	n/a
46	POLR2A	chr12:123469611-123469677	GM12878	blood:	n/a	n/a
47	POLR2A	chr12:123469118-123470607	ECC-1	luminal epithelium:	n/a	n/a
48	YY1	chr12:123469137-123469725	HepG2	liver:	n/a	n/a
49	POLR2A	chr12:123469129-123469692	MCF-7	breast:	n/a	n/a
50	POLR2A	chr12:123461706-123470094	K562	blood:	n/a	n/a

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:123469090..123471551-chr12:123505815..123507895,2	MCF-7	breast:
2	chr12:123467975..123470307-chr12:123638971..123640597,2	MCF-7	breast:
3	chr12:123468264..123470538-chr12:123712723..123715235,2	MCF-7	breast:
4	chr12:123467378..123471463-chr12:123484194..123486166,3	MCF-7	breast:
5	chr12:123467906..123470215-chr12:123495247..123497244,2	K562	blood:
6	chr12:123468471..123472230-chr12:123634537..123637693,4	K562	blood:
7	chr12:123469032..123471248-chr12:123684974..123687831,2	K562	blood:
8	chr12:123468080..123470439-chr12:123573373..123575937,2	K562	blood:
9	chr12:123469171..123471248-chr12:123684974..123686845,2	K562	blood:
10	chr12:123467368..123470978-chr12:123525099..123527744,3	K562	blood:
11	chr12:123356737..123358240-chr12:123467000..123469929,2	MCF-7	breast:

No data

Variant related genes	Relation type
ABCB9	TF binding region
ENSG00000265526	Chromatin interaction
ENSG00000090975	Chromatin interaction
ENSG00000051825	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1051434	0.96[CEU][hapmap]
rs10773921	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10848428	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs11060853	0.82[ASN][1000 genomes]
rs11608811	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11613937	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12425009	1.00[CEU][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12425850	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1727293	0.96[CEU][hapmap]
rs1727295	0.87[CEU][hapmap]
rs1727307	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs1790094	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs1790106	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs1790121	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs1790122	0.80[EUR][1000 genomes]
rs1984658	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28755851	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3759115	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3897102	0.98[ASN][1000 genomes]
rs4148862	0.81[EUR][1000 genomes]
rs4148863	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs4148866	0.81[ASN][1000 genomes]
rs4275659	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55742290	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61955196	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61955214	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7135296	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7296418	0.91[CEU][hapmap];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7305511	1.00[CEU][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7957096	0.96[CEU][hapmap];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs883562	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs884956	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs949143	1.00[CEU][hapmap];0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3388790	chr12:123275902-123655103	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv899572	chr12:123292503-123477311	Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv899573	chr12:123312051-123528405	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	nsv517200	chr12:123312051-123654498	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
5	nsv899576	chr12:123335527-123528405	Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
6	nsv832532	chr12:123395927-123573137	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
7	nsv832533	chr12:123395927-123589290	Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
8	nsv427924	chr12:123412172-123722059	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
9	nsv455732	chr12:123427573-123574838	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
10	nsv560492	chr12:123427573-123574838	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
11	nsv899577	chr12:123435248-123484474	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
12	nsv899578	chr12:123459005-123474529	Enhancers Transcr. at gene 5' and 3' Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
13	nsv560493	chr12:123467325-123479623	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs3741530	RP11-282O18.3	cis	Esophagus Mucosa	GTEx
rs3741530	CDK2AP1	cis	Esophagus Mucosa	GTEx
rs3741530	CDK2AP1	Cis_1M	lymphoblastoid	RTeQTL
rs3741530	MPHOSPH9	Cis_1M	lymphoblastoid	RTeQTL
rs3741530	ARL6IP4	Cis_1M	lymphoblastoid	RTeQTL
rs3741530	SBNO1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123461400-123473200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr12:123466000-123469800	Enhancers	Fetal Heart	heart
3	chr12:123466400-123470200	Genic enhancers	Cortex derived primary cultured neurospheres	brain
4	chr12:123466400-123473400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr12:123466600-123469800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
6	chr12:123466600-123470000	Genic enhancers	Lung	lung
7	chr12:123466600-123470000	Enhancers	Right Atrium	heart
8	chr12:123466600-123470600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr12:123466600-123471400	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr12:123466600-123483400	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr12:123466800-123469800	Enhancers	NH-A	brain
12	chr12:123466800-123470000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr12:123466800-123470200	Genic enhancers	Fetal Muscle Trunk	muscle
14	chr12:123466800-123470400	Genic enhancers	Fetal Stomach	stomach
15	chr12:123466800-123471000	Genic enhancers	Liver	Liver
16	chr12:123466800-123472000	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr12:123466800-123472400	Genic enhancers	Spleen	Spleen
18	chr12:123466800-123516000	Weak transcription	Small Intestine	intestine
19	chr12:123467000-123469800	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
20	chr12:123467000-123469800	Genic enhancers	Placenta	Placenta
21	chr12:123467000-123469800	Enhancers	HUVEC	blood vessel
22	chr12:123467000-123470200	Enhancers	Brain Angular Gyrus	brain
23	chr12:123467000-123470200	Genic enhancers	Fetal Muscle Leg	muscle
24	chr12:123467000-123470400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
25	chr12:123467000-123474000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr12:123467200-123469800	Genic enhancers	Fetal Intestine Large	intestine
27	chr12:123467200-123470000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr12:123467200-123470200	Genic enhancers	Fetal Thymus	thymus
29	chr12:123467200-123470200	Genic enhancers	NHLF	lung
30	chr12:123467400-123470000	Genic enhancers	Fetal Intestine Small	intestine
31	chr12:123467400-123472000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr12:123467600-123504000	Weak transcription	Hela-S3	cervix
33	chr12:123468000-123469800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr12:123468000-123469800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
35	chr12:123468000-123469800	Enhancers	Colon Smooth Muscle	Colon
36	chr12:123468000-123469800	Enhancers	HSMMtube	muscle
37	chr12:123468000-123470000	Enhancers	Muscle Satellite Cultured Cells	--
38	chr12:123468000-123470200	Enhancers	Brain Inferior Temporal Lobe	brain
39	chr12:123468000-123470200	Enhancers	Stomach Mucosa	stomach
40	chr12:123468000-123470400	Enhancers	Brain Substantia Nigra	brain
41	chr12:123468000-123470400	Enhancers	Fetal Lung	lung
42	chr12:123468000-123486200	Strong transcription	Fetal Brain Female	brain
43	chr12:123468200-123469800	Enhancers	Primary neutrophils fromperipheralblood	blood
44	chr12:123468200-123470000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr12:123468200-123470000	Enhancers	HSMM	muscle
46	chr12:123468200-123470000	Weak transcription	NHEK	skin
47	chr12:123468200-123470600	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr12:123468200-123470800	Weak transcription	Dnd41	blood
49	chr12:123468200-123471400	Weak transcription	HUES6 Cell Line	embryonic stem cell
50	chr12:123468200-123471800	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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