Variant report

Variant	rs2471342
Chromosome Location	chr4:3043420-3043421
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TBP	chr4:3042839-3044161	GM12878	blood:	n/a	n/a
2	YY1	chr4:3042831-3043485	GM12891	blood:	n/a	n/a
3	MTA3	chr4:3042029-3044138	GM12878	blood:	n/a	n/a
4	CTCF	chr4:3043228-3043447	H1-hESC	embryonic stem cell:	n/a	chr4:3043347-3043357
5	RCOR1	chr4:3043039-3043467	GM12878	blood:	n/a	n/a
6	POLR2A	chr4:3042210-3043957	GM18526	blood:	n/a	n/a
7	TAF1	chr4:3042966-3043921	GM12878	blood:	n/a	n/a
8	MAZ	chr4:3042927-3043926	GM12878	blood:	n/a	chr4:3043238-3043246
9	POLR2A	chr4:3042151-3043922	GM12892	blood:	n/a	n/a
10	POLR2A	chr4:3042989-3043872	GM12892	blood:	n/a	n/a
11	CTCF	chr4:3043320-3043470	HMEC	breast:	n/a	chr4:3043347-3043357
12	POLR2A	chr4:3042178-3044027	GM12892	blood:	n/a	n/a
13	CTCF	chr4:3043300-3043450	HepG2	liver:	n/a	chr4:3043347-3043357
14	CTCF	chr4:3043340-3043490	GM12871	blood:	n/a	chr4:3043347-3043357
15	EBF1	chr4:3042143-3043940	GM12878	blood:	n/a	chr4:3043105-3043116
16	RUNX3	chr4:3041924-3043896	GM12878	blood:	n/a	n/a
17	PAX5	chr4:3043122-3043442	GM12878	blood:	n/a	n/a
18	YY1	chr4:3043206-3043961	HepG2	liver:	n/a	chr4:3043534-3043548 chr4:3043511-3043525 chr4:3043525-3043539
19	ZNF143	chr4:3042943-3043669	GM12878	blood:	n/a	chr4:3043525-3043535
20	RUNX3	chr4:3041863-3044165	GM12878	blood:	n/a	n/a
21	POLR2A	chr4:3042215-3043929	GM18951	blood:	n/a	n/a
22	POLR2A	chr4:3042817-3043955	GM12891	blood:	n/a	n/a
23	CTCF	chr4:3043280-3043430	AG10803	skin:	n/a	chr4:3043347-3043357
24	POLR2A	chr4:3041640-3044734	GM12891	blood:	n/a	n/a
25	MAX	chr4:3043155-3043847	HepG2	liver:	n/a	chr4:3043238-3043246
26	POLR2A	chr4:3042157-3044616	GM12878	blood:	n/a	n/a
27	PAX5	chr4:3042120-3043907	GM12878	blood:	n/a	chr4:3042244-3042253
28	POLR2A	chr4:3042135-3044075	GM12878	blood:	n/a	n/a
29	POLR2A	chr4:3042204-3043918	GM10847	blood:	n/a	n/a
30	POLR2A	chr4:3042124-3044657	GM18505	blood:	n/a	n/a
31	POLR2A	chr4:3042827-3043934	GM12891	blood:	n/a	n/a
32	CTCF	chr4:3043280-3043430	SAEC	small airway:	n/a	chr4:3043347-3043357
33	POLR2A	chr4:3043085-3043941	HUVEC	blood vessel:	n/a	n/a
34	BHLHE40	chr4:3042034-3044019	GM12878	blood:	n/a	chr4:3043518-3043534 chr4:3043900-3043916 chr4:3043010-3043026
35	EBF1	chr4:3042948-3043710	GM12878	blood:	n/a	chr4:3043105-3043116
36	CHD1	chr4:3042158-3043826	GM12878	blood:	n/a	n/a
37	POLR2A	chr4:3042193-3044036	GM12892	blood:	n/a	n/a
38	ELF1	chr4:3042019-3044065	GM12878	blood:	n/a	chr4:3042273-3042285
39	STAT5A	chr4:3043307-3044252	GM12878	blood:	n/a	chr4:3043388-3043400 chr4:3044052-3044059
40	STAT5A	chr4:3042848-3043446	GM12878	blood:	n/a	chr4:3043388-3043400
41	POU2F2	chr4:3042918-3043998	GM12891	blood:	n/a	chr4:3043363-3043375 chr4:3043591-3043603
42	POLR2A	chr4:3042852-3043897	GM12878	blood:	n/a	n/a
43	POLR2A	chr4:3042174-3043956	GM12891	blood:	n/a	n/a
44	EBF1	chr4:3042931-3044004	GM12878	blood:	n/a	chr4:3043105-3043116
45	POU2F2	chr4:3042945-3043991	GM12891	blood:	n/a	chr4:3043363-3043375 chr4:3043591-3043603
46	POLR2A	chr4:3042829-3043945	GM12892	blood:	n/a	n/a
47	SMC3	chr4:3043219-3043435	GM12878	blood:	n/a	n/a
48	RELA	chr4:3042951-3043797	GM19099	blood:	n/a	n/a
49	CHD2	chr4:3042277-3043745	GM12878	blood:	n/a	n/a
50	MAX	chr4:3042171-3043968	GM12878	blood:	n/a	chr4:3043238-3043246

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:3038856..3040749-chr4:3043216..3045055,2	MCF-7	breast:
2	chr4:3038898..3040591-chr4:3042630..3044225,2	K562	blood:

Variant related genes	Relation type
RNU6-204P	TF binding region

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10021325	0.96[ASN][1000 genomes]
rs11929936	0.98[ASN][1000 genomes]
rs12506200	0.85[ASN][1000 genomes]
rs13141939	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13144633	0.98[ASN][1000 genomes]
rs34020100	0.87[ASN][1000 genomes]
rs34053308	0.96[ASN][1000 genomes]
rs34157939	0.98[ASN][1000 genomes]
rs34342095	0.94[ASN][1000 genomes]
rs34945363	0.98[ASN][1000 genomes]
rs35342954	0.96[ASN][1000 genomes]
rs35875899	0.98[ASN][1000 genomes]
rs61114397	0.81[ASN][1000 genomes]
rs61407336	0.96[ASN][1000 genomes]
rs7694687	0.91[ASN][1000 genomes]
rs7696040	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3418626	chr4:2741174-3461492	Genic enhancers Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	esv3397632	chr4:2741239-3460583	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv461163	chr4:2906285-3234980	Enhancers Strong transcription Flanking Active TSS Genic enhancers Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
4	nsv593437	chr4:2906285-3234980	Genic enhancers Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription 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	52 gene(s)	inside rSNPs	diseases
5	nsv1013440	chr4:2993130-3053503	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:3040600-3043600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr4:3041800-3044400	Flanking Active TSS	Primary B cells from peripheral blood	blood
3	chr4:3042200-3044400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
4	chr4:3042400-3044600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr4:3042400-3044600	Flanking Active TSS	GM12878-XiMat	blood
6	chr4:3042600-3043800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
7	chr4:3042600-3044000	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr4:3042600-3044000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr4:3042600-3044200	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
10	chr4:3042600-3044600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr4:3042600-3044600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
12	chr4:3042800-3043600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr4:3042800-3043600	Active TSS	Esophagus	oesophagus
14	chr4:3042800-3043600	Enhancers	Fetal Heart	heart
15	chr4:3042800-3044200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
16	chr4:3042800-3044200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
17	chr4:3042800-3044200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
18	chr4:3042800-3044200	Active TSS	Brain Cingulate Gyrus	brain
19	chr4:3042800-3044200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
20	chr4:3042800-3044200	Active TSS	Colon Smooth Muscle	Colon
21	chr4:3042800-3044200	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
22	chr4:3042800-3044200	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
23	chr4:3042800-3044200	Active TSS	Left Ventricle	heart
24	chr4:3042800-3044400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr4:3042800-3044400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr4:3042800-3044400	Active TSS	Brain Anterior Caudate	brain
27	chr4:3042800-3044400	Active TSS	Duodenum Smooth Muscle	Duodenum
28	chr4:3042800-3044400	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
29	chr4:3042800-3044600	Flanking Active TSS	Adipose Nuclei	Adipose
30	chr4:3042800-3044600	Active TSS	Pancreatic Islets	Pancreatic Islet
31	chr4:3042800-3044600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
32	chr4:3043000-3043600	Flanking Active TSS	Fetal Muscle Leg	muscle
33	chr4:3043000-3043600	Flanking Active TSS	Osteobl	bone
34	chr4:3043000-3043800	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
35	chr4:3043000-3043800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
36	chr4:3043000-3043800	Active TSS	Primary T killer memory cells from peripheral blood	blood
37	chr4:3043000-3043800	Active TSS	Placenta Amnion	Placenta Amnion
38	chr4:3043000-3043800	Flanking Active TSS	HMEC	breast
39	chr4:3043000-3044000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr4:3043000-3044000	Flanking Active TSS	Primary hematopoietic stem cells	blood
41	chr4:3043000-3044000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr4:3043000-3044000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr4:3043000-3044000	Flanking Bivalent TSS/Enh	Fetal Intestine Large	intestine
44	chr4:3043000-3044000	Bivalent Enhancer	Fetal Thymus	thymus
45	chr4:3043000-3044000	Active TSS	Pancreas	Pancrea
46	chr4:3043000-3044000	Active TSS	Right Ventricle	heart
47	chr4:3043000-3044000	Active TSS	Sigmoid Colon	Sigmoid Colon
48	chr4:3043000-3044000	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
49	chr4:3043000-3044000	Flanking Active TSS	HUVEC	blood vessel
50	chr4:3043000-3044200	Flanking Active TSS	Liver	Liver

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