Variant report

Variant	rs4534375
Chromosome Location	chr1:113286780-113286781
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:14)
CpG islands
(count:61)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:14 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr1:113286582-113287306	H1-hESC	embryonic stem cell:	n/a	n/a
2	USF2	chr1:113286653-113287147	H1-hESC	embryonic stem cell:	n/a	chr1:113286671-113286687
3	CHD2	chr1:113286755-113287177	H1-hESC	embryonic stem cell:	n/a	n/a
4	RCOR1	chr1:113286259-113287274	IMR90	lung:	n/a	n/a
5	BRCA1	chr1:113286700-113286893	H1-hESC	embryonic stem cell:	n/a	n/a
6	MAX	chr1:113286516-113287279	H1-hESC	embryonic stem cell:	n/a	n/a
7	CTCF	chr1:113286770-113287321	SK-N-SH	brain:	n/a	n/a
8	GABPA	chr1:113286552-113287182	H1-hESC	embryonic stem cell:	n/a	n/a
9	E2F6	chr1:113286653-113287340	H1-hESC	embryonic stem cell:	n/a	n/a
10	E2F6	chr1:113286248-113287368	H1-hESC	embryonic stem cell:	n/a	chr1:113286469-113286478
11	TBP	chr1:113286535-113287139	H1-hESC	embryonic stem cell:	n/a	n/a
12	RAD21	chr1:113286705-113287338	H1-hESC	embryonic stem cell:	n/a	chr1:113286907-113286920 chr1:113287104-113287117 chr1:113286707-113286719
13	CTCF	chr1:113286740-113286890	NHLF	lung:	n/a	n/a
14	BACH1	chr1:113286491-113287320	H1-hESC	embryonic stem cell:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:113286757-113286807	AoSMC	blood vessel:	n/a
2	chr1:113286757-113286807	AG10803	skin:	n/a
3	chr1:113286757-113286807	CMK	blood:	n/a
4	chr1:113286757-113286807	HRE	kidney:	n/a
5	chr1:113286757-113286807	ECC-1	luminal epithelium:	n/a
6	chr1:113286757-113286807	HepG2	liver:	n/a
7	chr1:113286757-113286807	HMEC	breast:	n/a
8	chr1:113286757-113286807	GM06990	blood:	n/a
9	chr1:113286757-113286807	HIPEpiC	eye:	n/a
10	chr1:113286757-113286807	SK-N-SH	brain:	n/a
11	chr1:113286757-113286807	HAEpiC	amniotic membrane:	n/a
12	chr1:113286757-113286807	H1-hESC	embryonic stem cell:	embryo
13	chr1:113286757-113286807	Hela-S3	cervix:	n/a
14	chr1:113286757-113286807	SK-N-SH_RA	brain:	n/a
15	chr1:113286757-113286807	HCT-116	colon:	n/a
16	chr1:113286757-113286807	HCPEpiC	choroid plexus:	n/a
17	chr1:113286757-113286807	AG04450	lung:	fetal
18	chr1:113286757-113286807	RPTEC	kidney:	n/a
19	chr1:113286757-113286807	HEK293	kidney:	embryo
20	chr1:113286757-113286807	NH-A	brain:	n/a
21	chr1:113286757-113286807	BE2_C	brain:	n/a
22	chr1:113286757-113286807	NT2-D1	testis:	n/a
23	chr1:113286757-113286807	ProgFib	skin:	n/a
24	chr1:113286757-113286807	NHDF-neo	bronchial:	n/a
25	chr1:113286757-113286807	PANC-1	pancreas:	n/a
26	chr1:113286757-113286807	SKMC	muscle:	n/a
27	chr1:113286757-113286807	AG09319	gingival:	n/a
28	chr1:113286757-113286807	NHBE	bronchial:	n/a
29	chr1:113286757-113286807	HL-60	blood:	n/a
30	chr1:113286757-113286807	A549	lung:	n/a
31	chr1:113286757-113286807	BJ	skin:	n/a
32	chr1:113286757-113286807	AG04449	skin:	fetal
33	chr1:113286757-113286807	HUVEC	blood vessel:	n/a
34	chr1:113286757-113286807	HNPCEpiC	eye:	n/a
35	chr1:113286757-113286807	Hepatocyte	liver:	n/a
36	chr1:113286757-113286807	SAEC	small airway:	n/a
37	chr1:113286757-113286807	HEEpiC	esophagus:	n/a
38	chr1:113286757-113286807	GM12878	blood:	n/a
39	chr1:113286757-113286807	MCF-7	breast:	n/a
40	chr1:113286757-113286807	PrEC	prostate:	n/a
41	chr1:113286757-113286807	AG09309	skin:	n/a
42	chr1:113286757-113286807	PFSK-1	brain:	n/a
43	chr1:113286757-113286807	LNCaP	prostate:	n/a
44	chr1:113286757-113286807	HRPEpiC	eye:	n/a
45	chr1:113286757-113286807	Caco-2	colon:	n/a
46	chr1:113286757-113286807	SK-N-MC	brain:	n/a
47	chr1:113286757-113286807	HCM	heart:	n/a
48	chr1:113286757-113286807	GM19239	blood:	n/a
49	chr1:113286757-113286807	HPAEpiC	pulmonary alveolar:	n/a
50	chr1:113286757-113286807	T-47D	breast:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:113285199..113288052-chr1:113290099..113291862,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000234790	TF binding region
ENSG00000234790	CpG island
ENSG00000234790	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11584214	0.92[ASN][1000 genomes]
rs34532657	0.87[ASN][1000 genomes]
rs4317803	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4381183	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4534376	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61220461	0.80[ASN][1000 genomes]
rs6682219	0.81[JPT][hapmap]
rs6683234	0.89[ASN][1000 genomes]
rs6685749	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68020961	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72701137	0.97[ASN][1000 genomes]
rs7553091	0.80[ASN][1000 genomes]
rs7555319	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002971	chr1:112924725-113740584	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong 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	166 gene(s)	inside rSNPs	diseases
2	nsv535059	chr1:112924725-113740584	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
3	nsv1010276	chr1:113123932-113740584	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised 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 miRNA target site	158 gene(s)	inside rSNPs	diseases
4	nsv533295	chr1:113167645-113589588	Flanking Active TSS Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
5	nsv1012119	chr1:113214869-113759081	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
6	nsv535060	chr1:113214869-113759081	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
7	nsv529238	chr1:113229946-113759080	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	100 gene(s)	inside rSNPs	diseases
8	esv18511	chr1:113246318-113350775	Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
9	nsv998794	chr1:113246630-113310418	Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
10	nsv547566	chr1:113248365-113301657	Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
11	nsv818378	chr1:113263711-113434818	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4534375	KCND3	cis	cerebellum	SCAN

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113285600-113286800	Weak transcription	Pancreas	Pancrea
2	chr1:113285800-113287000	Bivalent Enhancer	Fetal Heart	heart
3	chr1:113285800-113287200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
4	chr1:113285800-113287200	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr1:113286200-113286800	Bivalent Enhancer	Fetal Intestine Large	intestine
6	chr1:113286200-113287000	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
7	chr1:113286200-113287000	Bivalent Enhancer	Lung	lung
8	chr1:113286200-113287200	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
9	chr1:113286200-113287200	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
10	chr1:113286200-113287200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
11	chr1:113286200-113287200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
12	chr1:113286200-113287200	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr1:113286200-113287200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr1:113286200-113287200	Bivalent Enhancer	Primary B cells from peripheral blood	blood
15	chr1:113286200-113287200	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
16	chr1:113286200-113287200	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
17	chr1:113286200-113287200	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr1:113286200-113287200	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr1:113286200-113287200	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr1:113286200-113287200	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr1:113286200-113287200	Bivalent/Poised TSS	Brain Germinal Matrix	brain
22	chr1:113286200-113287200	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
23	chr1:113286200-113287200	Flanking Bivalent TSS/Enh	Esophagus	oesophagus
24	chr1:113286200-113287400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
25	chr1:113286200-113287400	Bivalent/Poised TSS	NHDF-Ad	bronchial
26	chr1:113286200-113287400	Bivalent/Poised TSS	NHEK	skin
27	chr1:113286400-113286800	Flanking Bivalent TSS/Enh	Breast Myoepithelial Primary Cells	Breast
28	chr1:113286400-113286800	Bivalent Enhancer	Primary T cells from cord blood	blood
29	chr1:113286400-113286800	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
30	chr1:113286400-113286800	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr1:113286400-113286800	Bivalent Enhancer	Fetal Intestine Small	intestine
32	chr1:113286400-113286800	Bivalent Enhancer	Placenta	Placenta
33	chr1:113286400-113286800	Flanking Active TSS	Right Atrium	heart
34	chr1:113286400-113286800	Flanking Bivalent TSS/Enh	Osteobl	bone
35	chr1:113286400-113287000	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
36	chr1:113286400-113287000	Bivalent/Poised TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr1:113286400-113287000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
38	chr1:113286400-113287000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
39	chr1:113286400-113287000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr1:113286400-113287000	Bivalent/Poised TSS	Primary T helper naive cells fromperipheralblood	blood
41	chr1:113286400-113287000	Flanking Bivalent TSS/Enh	Muscle Satellite Cultured Cells	--
42	chr1:113286400-113287000	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr1:113286400-113287000	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
44	chr1:113286400-113287000	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
45	chr1:113286400-113287000	Active TSS	Ovary	ovary
46	chr1:113286400-113287000	Flanking Bivalent TSS/Enh	Placenta Amnion	Placenta Amnion
47	chr1:113286400-113287000	Flanking Active TSS	Right Ventricle	heart
48	chr1:113286400-113287000	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
49	chr1:113286400-113287000	Bivalent Enhancer	Stomach Mucosa	stomach
50	chr1:113286400-113287000	Enhancers	Spleen	Spleen

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