Variant report

Variant	rs2530594
Chromosome Location	chr4:3250754-3250755
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:183)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr4:3250731-3251184	K562	blood:	n/a	chr4:3250816-3250825
2	POLR2A	chr4:3250388-3251359	H1-neurons	neurons:	n/a	n/a
3	GABPA	chr4:3250743-3251099	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr4:3250466-3251221	H1-neurons	neurons:	n/a	n/a
5	REST	chr4:3250520-3251207	H1-neurons	neurons:	n/a	chr4:3250906-3250916
6	REST	chr4:3250246-3251303	H1-neurons	neurons:	n/a	chr4:3250906-3250916

(count:183 , 50 per page) page: 1 2 3 4

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr4:3250726-3250776	AoSMC	blood vessel:	n/a
2	chr4:3250726-3250776	HEEpiC	esophagus:	n/a
3	chr4:3250745-3250795	GM06990	blood:	n/a
4	chr4:3250745-3250795	HIPEpiC	eye:	n/a
5	chr4:3250745-3250795	SK-N-MC	brain:	n/a
6	chr4:3250722-3250772	AG04450	lung:	fetal
7	chr4:3250745-3250795	HAEpiC	amniotic membrane:	n/a
8	chr4:3250722-3250772	Caco-2	colon:	n/a
9	chr4:3250745-3250795	SK-N-SH_RA	brain:	n/a
10	chr4:3250745-3250795	HEK293	kidney:	embryo
11	chr4:3250722-3250772	ProgFib	skin:	n/a
12	chr4:3250745-3250795	HepG2	liver:	n/a
13	chr4:3250722-3250772	K562	blood:	n/a
14	chr4:3250722-3250772	Hela-S3	cervix:	n/a
15	chr4:3250722-3250772	GM12878	blood:	n/a
16	chr4:3250722-3250772	HRCEpiC	kidney:	n/a
17	chr4:3250722-3250772	PFSK-1	brain:	n/a
18	chr4:3250745-3250795	GM19239	blood:	n/a
19	chr4:3250726-3250776	BE2_C	brain:	n/a
20	chr4:3250726-3250776	CMK	blood:	n/a
21	chr4:3250726-3250776	AG04449	skin:	fetal
22	chr4:3250726-3250776	ovcar-3	ovarian:	n/a
23	chr4:3250722-3250772	SKMC	muscle:	n/a
24	chr4:3250726-3250776	LNCaP	prostate:	n/a
25	chr4:3250726-3250776	HNPCEpiC	eye:	n/a
26	chr4:3250745-3250795	HCF	heart:	n/a
27	chr4:3250722-3250772	RPTEC	kidney:	n/a
28	chr4:3250722-3250772	H1-hESC	embryonic stem cell:	embryo
29	chr4:3250726-3250776	ECC-1	luminal epithelium:	n/a
30	chr4:3250722-3250772	AG10803	skin:	n/a
31	chr4:3250726-3250776	SK-N-SH_RA	brain:	n/a
32	chr4:3250722-3250772	MCF10A-Er-Src	breast:	n/a
33	chr4:3250726-3250776	HPAEpiC	pulmonary alveolar:	n/a
34	chr4:3250722-3250772	HCF	heart:	n/a
35	chr4:3250745-3250795	NB4	blood:	n/a
36	chr4:3250726-3250776	RPTEC	kidney:	n/a
37	chr4:3250745-3250795	SK-N-SH	brain:	n/a
38	chr4:3250726-3250776	HUVEC	blood vessel:	n/a
39	chr4:3250745-3250795	HCM	heart:	n/a
40	chr4:3250726-3250776	SK-N-SH	brain:	n/a
41	chr4:3250722-3250772	HIPEpiC	eye:	n/a
42	chr4:3250726-3250776	PrEC	prostate:	n/a
43	chr4:3250726-3250776	H1-hESC	embryonic stem cell:	embryo
44	chr4:3250745-3250795	HUVEC	blood vessel:	n/a
45	chr4:3250726-3250776	NH-A	brain:	n/a
46	chr4:3250726-3250776	HIPEpiC	eye:	n/a
47	chr4:3250745-3250795	T-47D	breast:	n/a
48	chr4:3250745-3250795	AG10803	skin:	n/a
49	chr4:3250722-3250772	LNCaP	prostate:	n/a
50	chr4:3250745-3250795	IMR90	lung:	fetal

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:3249484..3252398-chr4:3294414..3296079,2	K562	blood:

No data

Variant related genes	Relation type
MSANTD1	TF binding region
MSANTD1	CpG island
ENSG00000159788	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs3025816	1.00[CHD][hapmap]
rs7657430	1.00[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 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	nsv998290	chr4:3176454-3355758	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv524211	chr4:3215835-3270488	Strong transcription Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
5	nsv470003	chr4:3215835-3275484	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
6	nsv878454	chr4:3215835-3305739	Active TSS Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
7	nsv878455	chr4:3215835-3344891	Strong transcription Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS 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	10 gene(s)	inside rSNPs	diseases
8	nsv878456	chr4:3215835-3467519	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
9	nsv428106	chr4:3226182-3752322	Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
10	nsv878457	chr4:3231661-3278517	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
11	nsv878458	chr4:3235518-3303976	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
12	nsv878459	chr4:3235518-3310831	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:3114600-3292400	Weak transcription	Right Atrium	heart
2	chr4:3238000-3259200	Weak transcription	HSMMtube	muscle
3	chr4:3238200-3255200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr4:3238200-3261400	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr4:3238600-3259800	Weak transcription	NH-A	brain
6	chr4:3241600-3259200	Weak transcription	Small Intestine	intestine
7	chr4:3242200-3252000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr4:3243000-3260000	Weak transcription	Brain Angular Gyrus	brain
9	chr4:3243200-3251400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr4:3243400-3252000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr4:3243400-3254400	Weak transcription	GM12878-XiMat	blood
12	chr4:3243400-3259200	Weak transcription	Colonic Mucosa	Colon
13	chr4:3243400-3259600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr4:3243600-3258800	Weak transcription	Primary B cells from peripheral blood	blood
15	chr4:3243800-3257400	Weak transcription	Gastric	stomach
16	chr4:3243800-3258000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr4:3244000-3252200	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr4:3244000-3252200	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr4:3244200-3252400	Weak transcription	Fetal Intestine Large	intestine
20	chr4:3244200-3259400	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr4:3244400-3252000	Weak transcription	Fetal Lung	lung
22	chr4:3244800-3251200	Weak transcription	Brain Anterior Caudate	brain
23	chr4:3244800-3259600	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr4:3245000-3255400	Weak transcription	Esophagus	oesophagus
25	chr4:3245200-3251800	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr4:3245200-3255000	Weak transcription	Pancreas	Pancrea
27	chr4:3245200-3259800	Weak transcription	Primary T helper cells PMA-I stimulated	--
28	chr4:3245200-3260000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr4:3245400-3256600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr4:3245400-3257800	Weak transcription	Primary T helper cells fromperipheralblood	blood
31	chr4:3245400-3259200	Weak transcription	Ovary	ovary
32	chr4:3245600-3252200	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr4:3245600-3252200	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr4:3245600-3253000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr4:3245600-3255000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr4:3246000-3255000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr4:3246200-3251800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr4:3246200-3258600	Weak transcription	Duodenum Mucosa	Duodenum
39	chr4:3246400-3252000	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr4:3246400-3254000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr4:3246400-3255000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr4:3246400-3261000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr4:3246600-3250800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr4:3246600-3254800	Weak transcription	Liver	Liver
45	chr4:3246600-3256200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr4:3246600-3257400	Weak transcription	Right Ventricle	heart
47	chr4:3246600-3257800	Weak transcription	Adipose Nuclei	Adipose
48	chr4:3246600-3261400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr4:3247000-3252000	Weak transcription	Fetal Intestine Small	intestine
50	chr4:3247000-3255000	Weak transcription	Lung	lung

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