Variant report

Variant	rs59556423
Chromosome Location	chr3:50359845-50359846
allele	C/T
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	CTCF	chr3:50359740-50359890	SK-N-SH_RA	brain:	n/a	n/a
2	POLR2A	chr3:50358170-50360519	HUVEC	blood vessel:	n/a	n/a
3	CTCF	chr3:50359780-50359930	WERI-Rb-1	eye:	n/a	n/a
4	POLR2A	chr3:50358223-50362338	HUVEC	blood vessel:	n/a	n/a
5	POLR2A	chr3:50358105-50360508	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr3:50353534-50362749	HUVEC	blood vessel:	n/a	n/a
7	REST	chr3:50357851-50359910	H1-neurons	neurons:	n/a	chr3:50359493-50359506
8	CHD1	chr3:50359790-50359914	H1-hESC	embryonic stem cell:	n/a	n/a
9	SIN3A	chr3:50358047-50360497	H1-hESC	embryonic stem cell:	n/a	chr3:50358629-50358640 chr3:50359896-50359909 chr3:50360384-50360397 chr3:50358604-50358615 chr3:50359295-50359303 chr3:50360182-50360195
10	CTCF	chr3:50359824-50359910	GM12891	blood:	n/a	n/a
11	MAX	chr3:50357339-50360793	HepG2	liver:	n/a	chr3:50360294-50360303 chr3:50359499-50359509 chr3:50358671-50358680
12	CTCF	chr3:50359780-50359930	HAc	cerebellar:	n/a	n/a
13	CTCF	chr3:50359820-50359970	HCM	heart:	n/a	n/a
14	POLR2A	chr3:50357654-50360859	HepG2	liver:	n/a	n/a
15	POLR2A	chr3:50355509-50362517	HepG2	liver:	n/a	n/a
16	POLR2A	chr3:50356481-50362357	HUVEC	blood vessel:	n/a	n/a
17	GTF3C2	chr3:50357980-50359877	K562	blood:	n/a	n/a
18	TBP	chr3:50358228-50360361	H1-hESC	embryonic stem cell:	n/a	n/a
19	POLR2A	chr3:50357472-50360583	H1-hESC	embryonic stem cell:	n/a	n/a
20	POLR2A	chr3:50356930-50359873	SK-N-MC	brain:	n/a	n/a
21	POLR2A	chr3:50359829-50360079	H1-hESC	embryonic stem cell:	n/a	n/a
22	CTCF	chr3:50359780-50359930	GM12875	blood:	n/a	n/a
23	POLR2A	chr3:50356933-50362245	HUVEC	blood vessel:	n/a	n/a
24	POLR2A	chr3:50359780-50360372	H1-hESC	embryonic stem cell:	n/a	n/a
25	CREB1	chr3:50358115-50359846	HepG2	liver:	n/a	n/a
26	CTCF	chr3:50359700-50359850	HRE	kidney:	n/a	n/a
27	CTCF	chr3:50359760-50359910	HRE	kidney:	n/a	n/a
28	CTCF	chr3:50358107-50360081	SK-N-SH	brain:	n/a	chr3:50359284-50359302 chr3:50360011-50360032
29	POLR2A	chr3:50359700-50360544	PFSK-1	brain:	n/a	n/a
30	CTCF	chr3:50359820-50359970	HPAF	blood vessel:	n/a	n/a
31	MAZ	chr3:50358123-50360111	IMR90	lung:	n/a	chr3:50359499-50359509 chr3:50358671-50358680
32	CTCF	chr3:50359800-50359950	HBMEC	blood vessel:	n/a	n/a
33	CTCF	chr3:50359780-50359930	HUVEC	blood vessel:	n/a	n/a
34	EGR1	chr3:50358219-50359963	HCT-116	colon:	n/a	chr3:50358692-50358705 chr3:50358655-50358669 chr3:50358656-50358669 chr3:50358656-50358669 chr3:50358653-50358667 chr3:50358656-50358669 chr3:50359493-50359503 chr3:50358597-50358610 chr3:50359247-50359257 chr3:50358786-50358799 chr3:50359248-50359258 chr3:50358657-50358666 chr3:50358655-50358670 chr3:50358656-50358669 chr3:50359249-50359259 chr3:50358656-50358666 chr3:50359438-50359448 chr3:50358594-50358608
35	TAF1	chr3:50358274-50360441	H1-hESC	embryonic stem cell:	n/a	n/a
36	CTCF	chr3:50359800-50359950	HUVEC	blood vessel:	n/a	n/a
37	POLR2A	chr3:50357855-50362316	HUVEC	blood vessel:	n/a	n/a
38	CHD2	chr3:50358655-50359880	H1-hESC	embryonic stem cell:	n/a	chr3:50358794-50358804

No.	Distal block	Cell Line	Cell type
1	chr3:50324564..50342616-chr3:50350801..50362499,49	MCF-7	breast:
2	chr3:50327926..50342388-chr3:50350886..50359960,36	MCF-7	breast:
3	chr3:50286473..50289840-chr3:50357894..50361890,3	MCF-7	breast:
4	chr3:50300460..50314689-chr3:50349154..50363682,34	MCF-7	breast:
5	chr3:50326497..50328403-chr3:50359126..50362174,3	K562	blood:
6	chr3:50328785..50330512-chr3:50359361..50362039,2	K562	blood:
7	chr3:50359840..50362158-chr3:50378433..50381036,4	MCF-7	breast:
8	chr3:50295790..50299500-chr3:50356173..50362991,11	MCF-7	breast:
9	chr3:50296091..50300659-chr3:50356103..50362246,11	MCF-7	breast:
10	chr3:50334885..50342502-chr3:50352987..50366859,26	K562	blood:
11	chr3:50307238..50313479-chr3:50353130..50365794,18	MCF-7	breast:
12	chr3:50356822..50362778-chr3:50372728..50378128,10	MCF-7	breast:
13	chr3:50315023..50318386-chr3:50356939..50360295,5	MCF-7	breast:
14	chr3:50309725..50313756-chr3:50357883..50363910,8	K562	blood:
15	chr3:50326497..50331702-chr3:50356299..50362839,8	K562	blood:
16	chr3:50273624..50275186-chr3:50358650..50361013,3	MCF-7	breast:
17	chr3:50334334..50341950-chr3:50357130..50360296,11	K562	blood:
18	chr3:50358941..50361701-chr3:50396606..50398793,2	MCF-7	breast:
19	chr3:50357891..50360438-chr3:50381704..50384677,2	MCF-7	breast:
20	chr3:50311192..50313650-chr3:50358965..50360786,3	K562	blood:

Variant related genes	Relation type
HYAL2	TF binding region
ENSG00000235058	Chromatin interaction
ENSG00000004838	Chromatin interaction
ENSG00000230454	Chromatin interaction
ENSG00000068028	Chromatin interaction
ENSG00000114353	Chromatin interaction
ENSG00000012171	Chromatin interaction
ENSG00000179564	Chromatin interaction
ENSG00000214706	Chromatin interaction
ENSG00000232352	Chromatin interaction
ENSG00000243477	Chromatin interaction
ENSG00000186792	Chromatin interaction
ENSG00000126062	Chromatin interaction
ENSG00000114378	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs12490837	0.94[AFR][1000 genomes]
rs2229647	0.97[AFR][1000 genomes]
rs2233476	0.91[AFR][1000 genomes]
rs2233482	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2236946	0.83[AFR][1000 genomes]
rs35587949	0.89[AFR][1000 genomes]
rs4688679	0.91[AFR][1000 genomes]
rs4688728	0.89[AFR][1000 genomes]
rs4688736	0.97[AFR][1000 genomes]
rs58780990	1.00[AMR][1000 genomes]
rs59476380	0.86[AFR][1000 genomes]
rs60983897	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61275090	1.00[AMR][1000 genomes]
rs61689858	1.00[AMR][1000 genomes]
rs61737738	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72932956	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72932962	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72932964	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72932983	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72934803	1.00[AMR][1000 genomes]
rs72934806	1.00[AMR][1000 genomes]
rs72934814	1.00[AMR][1000 genomes]
rs72934815	1.00[AMR][1000 genomes]
rs72934824	1.00[AMR][1000 genomes]
rs72934827	1.00[AMR][1000 genomes]
rs72934830	1.00[AMR][1000 genomes]
rs928946	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv523662	chr3:50144951-50584999	Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
2	nsv876769	chr3:50155468-50408398	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription 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	94 gene(s)	inside rSNPs	diseases
3	esv1821728	chr3:50156142-50657253	Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
4	esv1793751	chr3:50157364-50476363	Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
5	esv1828162	chr3:50157364-50506151	Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
6	nsv470561	chr3:50158774-50584999	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
7	nsv876770	chr3:50158774-50609624	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
8	nsv1001993	chr3:50187646-50640808	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
9	esv2757870	chr3:50198478-50371377	Genic enhancers Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
10	esv2759148	chr3:50198478-50371377	Enhancers Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
11	nsv834692	chr3:50198485-50393464	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
12	nsv590254	chr3:50243510-50388607	Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
13	nsv460531	chr3:50247824-50436827	Strong transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
14	nsv590255	chr3:50247824-50436827	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
15	nsv876772	chr3:50255305-50436827	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
16	nsv590257	chr3:50302830-50393640	Genic enhancers Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
17	nsv590256	chr3:50302830-50420554	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' 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	83 gene(s)	inside rSNPs	diseases
18	nsv876774	chr3:50302830-50436827	Enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
19	nsv876773	chr3:50302830-50480131	Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
20	nsv834693	chr3:50302830-50507964	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
21	nsv876775	chr3:50324672-50504896	Flanking Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS 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	82 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50357800-50360200	Active TSS	iPS-18 Cell Line	embryonic stem cell
2	chr3:50357800-50360200	Active TSS	Fetal Kidney	kidney
3	chr3:50357800-50360200	Active TSS	Pancreatic Islets	Pancreatic Islet
4	chr3:50357800-50360400	Active TSS	H9 Cell Line	embryonic stem cell
5	chr3:50357800-50360400	Active TSS	iPS-15b Cell Line	embryonic stem cell
6	chr3:50357800-50360400	Active TSS	iPS-20b Cell Line	embryonic stem cell
7	chr3:50358000-50360200	Active TSS	HUES48 Cell Line	embryonic stem cell
8	chr3:50358000-50360400	Active TSS	ES-I3 Cell Line	embryonic stem cell
9	chr3:50358000-50360400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
10	chr3:50358000-50360400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr3:50358000-50360400	Active TSS	Psoas Muscle	Psoas
12	chr3:50358200-50360000	Active TSS	HUES6 Cell Line	embryonic stem cell
13	chr3:50358200-50360200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr3:50358200-50360200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
15	chr3:50358200-50360200	Active TSS	Esophagus	oesophagus
16	chr3:50358200-50360200	Active TSS	Ovary	ovary
17	chr3:50358200-50360200	Active TSS	NHLF	lung
18	chr3:50358200-50360400	Active TSS	HUES64 Cell Line	embryonic stem cell
19	chr3:50358400-50360200	Active TSS	HUVEC	blood vessel
20	chr3:50359000-50360000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr3:50359000-50360000	Flanking Active TSS	Fetal Thymus	thymus
22	chr3:50359000-50360400	Flanking Active TSS	Placenta	Placenta
23	chr3:50359200-50360000	Flanking Active TSS	Brain Cingulate Gyrus	brain
24	chr3:50359200-50360200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
25	chr3:50359200-50360400	Enhancers	Fetal Brain Male	brain
26	chr3:50359200-50360400	Flanking Active TSS	Fetal Muscle Leg	muscle
27	chr3:50359200-50360400	Flanking Active TSS	Fetal Stomach	stomach
28	chr3:50359200-50360400	Flanking Active TSS	Pancreas	Pancrea
29	chr3:50359200-50360600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr3:50359200-50360600	Flanking Active TSS	Fetal Muscle Trunk	muscle
31	chr3:50359200-50360600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
32	chr3:50359200-50361000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
33	chr3:50359200-50362000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
34	chr3:50359400-50360000	Flanking Active TSS	Primary hematopoietic stem cells	blood
35	chr3:50359400-50360000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr3:50359400-50360000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr3:50359400-50360000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr3:50359400-50360000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr3:50359400-50360000	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
40	chr3:50359400-50360000	Enhancers	NH-A	brain
41	chr3:50359400-50360200	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr3:50359400-50360200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr3:50359400-50360200	Flanking Active TSS	Brain Germinal Matrix	brain
44	chr3:50359400-50360200	Flanking Active TSS	Fetal Intestine Large	intestine
45	chr3:50359400-50360200	Flanking Active TSS	Fetal Intestine Small	intestine
46	chr3:50359400-50360200	Flanking Active TSS	Lung	lung
47	chr3:50359400-50360200	Flanking Active TSS	Hela-S3	cervix
48	chr3:50359400-50360400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr3:50359400-50360400	Flanking Active TSS	Brain Hippocampus Middle	brain
50	chr3:50359400-50360400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain

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