Variant report

Variant	rs3986354
Chromosome Location	chr15:40330876-40330877
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	MTA3	chr15:40330815-40331994	GM12878	blood:	n/a	n/a
2	POLR2A	chr15:40330490-40331825	PFSK-1	brain:	n/a	n/a
3	SIN3AK20	chr15:40330713-40331902	MCF-7	breast:	n/a	n/a
4	GABPA	chr15:40330707-40331988	SK-N-SH	brain:	n/a	chr15:40331471-40331480
5	ELF1	chr15:40330662-40331642	GM12878	blood:	n/a	chr15:40331363-40331376 chr15:40331366-40331375 chr15:40331365-40331376
6	MAZ	chr15:40330539-40331790	K562	blood:	n/a	chr15:40331461-40331471
7	POLR2A	chr15:40330079-40331716	H1-hESC	embryonic stem cell:	n/a	n/a
8	GABPA	chr15:40330872-40331859	MCF-7	breast:	n/a	chr15:40331471-40331480
9	POLR2A	chr15:40330838-40331904	PFSK-1	brain:	n/a	n/a
10	TAF1	chr15:40330439-40331765	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr15:40330399-40331753	Hela-S3	cervix:	n/a	n/a
12	ZC3H11A	chr15:40330806-40330951	K562	blood:	n/a	n/a
13	SIN3AK20	chr15:40330754-40331487	H1-hESC	embryonic stem cell:	n/a	n/a
14	MAZ	chr15:40330403-40331770	IMR90	lung:	n/a	chr15:40331461-40331471
15	MAX	chr15:40330731-40331663	K562	blood:	n/a	chr15:40331461-40331471
16	CTCF	chr15:40330740-40330890	RPTEC	kidney:	n/a	n/a
17	POLR2A	chr15:40330654-40331916	K562	blood:	n/a	n/a
18	TCF7L2	chr15:40330721-40330938	Hela-S3	cervix:	n/a	n/a
19	GABPA	chr15:40330649-40331947	A549	lung:	n/a	chr15:40331471-40331480
20	RAD21	chr15:40330454-40331598	IMR90	lung:	n/a	chr15:40331219-40331233
21	MXI1	chr15:40330015-40331992	SK-N-SH	brain:	n/a	n/a
22	KAP1	chr15:40330768-40331775	HEK293	kidney:	n/a	n/a
23	MAX	chr15:40330871-40331989	ECC-1	luminal epithelium:	n/a	chr15:40331461-40331471
24	POLR2A	chr15:40330825-40331905	HUVEC	blood vessel:	n/a	n/a
25	POLR2A	chr15:40330638-40331835	MCF10A-Er-Src	breast:	n/a	n/a
26	TBP	chr15:40330834-40331670	H1-hESC	embryonic stem cell:	n/a	n/a
27	JUND	chr15:40330519-40330891	H1-hESC	embryonic stem cell:	n/a	n/a
28	TAF1	chr15:40330564-40331671	H1-neurons	neurons:	n/a	n/a
29	GABPA	chr15:40330834-40331926	HL-60	blood:	n/a	chr15:40331471-40331480
30	SIN3AK20	chr15:40330774-40331622	PANC-1	pancreas:	n/a	n/a
31	ATF2	chr15:40330390-40330982	H1-hESC	embryonic stem cell:	n/a	n/a
32	POLR2A	chr15:40330430-40331801	H1-neurons	neurons:	n/a	n/a
33	POLR2A	chr15:40330815-40331756	GM12892	blood:	n/a	n/a
34	POLR2A	chr15:40329864-40331947	SK-N-MC	brain:	n/a	n/a
35	POLR2A	chr15:40330547-40330921	H1-hESC	embryonic stem cell:	n/a	n/a
36	POLR2A	chr15:40330394-40331991	GM12878	blood:	n/a	n/a
37	POLR2A	chr15:40330448-40331739	H1-neurons	neurons:	n/a	n/a
38	CTCF	chr15:40330760-40330910	AG04449	skin:	n/a	n/a
39	POLR2A	chr15:40330835-40331752	K562	blood:	n/a	n/a
40	SMC3	chr15:40330493-40331889	Hela-S3	cervix:	n/a	chr15:40331225-40331235 chr15:40331488-40331498
41	POLR2A	chr15:40330727-40331710	K562	blood:	n/a	n/a
42	HCFC1	chr15:40329972-40331977	Hela-S3	cervix:	n/a	n/a
43	MXI1	chr15:40330541-40331727	HepG2	liver:	n/a	n/a
44	POLR2A	chr15:40330525-40331743	Hela-S3	cervix:	n/a	n/a
45	POLR2A	chr15:40330873-40331864	ProgFib	skin:	n/a	n/a
46	REST	chr15:40330225-40332007	H1-neurons	neurons:	n/a	n/a
47	POLR2A	chr15:40329974-40331862	SK-N-SH	brain:	n/a	n/a
48	SMARCB1	chr15:40330804-40331644	Hela-S3	cervix:	n/a	n/a
49	POLR2A	chr15:40330863-40331928	HepG2	liver:	n/a	n/a
50	PML	chr15:40330874-40331783	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:40329348..40332922-chr15:40394377..40398986,5	MCF-7	breast:
2	chr15:40074208..40076102-chr15:40329673..40331654,2	K562	blood:
3	chr15:40328437..40331273-chr15:40400158..40402046,2	MCF-7	breast:
4	chr15:40320931..40323149-chr15:40329689..40332182,2	MCF-7	breast:
5	chr15:40330444..40331444-chr19:10262213..10263005,2	NB4	blood:

Variant related genes	Relation type
SRP14-AS1	TF binding region
ENSG00000150667	Chromatin interaction
ENSG00000130816	Chromatin interaction
ENSG00000128829	Chromatin interaction
ENSG00000104081	Chromatin interaction
ENSG00000261136	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs12441342	0.80[ASN][1000 genomes]
rs2291622	0.91[CHB][hapmap];0.96[JPT][hapmap];0.81[AMR][1000 genomes]
rs2898985	0.87[CHB][hapmap];0.95[JPT][hapmap]
rs4432245	0.87[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes]
rs4594236	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs4924407	0.89[EUR][1000 genomes]
rs4924408	0.89[EUR][1000 genomes]
rs711906	0.87[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes]
rs7496663	0.82[AMR][1000 genomes]
rs8042947	0.95[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530816	chr15:40003136-40586792	Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS 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	nsv428635	chr15:40274500-40436293	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 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	chr15:40330000-40331400	Flanking Active TSS	Primary hematopoietic stem cells	blood
2	chr15:40330000-40331400	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
3	chr15:40330000-40332000	Active TSS	H9 Cell Line	embryonic stem cell
4	chr15:40330000-40332000	Active TSS	Ovary	ovary
5	chr15:40330000-40332200	Active TSS	Left Ventricle	heart
6	chr15:40330000-40332400	Active TSS	Right Atrium	heart
7	chr15:40330200-40331000	Flanking Active TSS	Primary B cells from cord blood	blood
8	chr15:40330200-40331000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
9	chr15:40330200-40331000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr15:40330200-40331000	Transcr. at gene 5' and 3'	Fetal Muscle Leg	muscle
11	chr15:40330200-40331000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
12	chr15:40330200-40331400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
13	chr15:40330200-40331800	Active TSS	Small Intestine	intestine
14	chr15:40330200-40332000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
15	chr15:40330200-40332000	Active TSS	iPS-18 Cell Line	embryonic stem cell
16	chr15:40330200-40332000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
17	chr15:40330200-40332000	Active TSS	Breast Myoepithelial Primary Cells	Breast
18	chr15:40330200-40332000	Active TSS	Gastric	stomach
19	chr15:40330200-40332200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr15:40330200-40332200	Active TSS	NHDF-Ad	bronchial
21	chr15:40330200-40332200	Active TSS	NHLF	lung
22	chr15:40330200-40332400	Active TSS	Colonic Mucosa	Colon
23	chr15:40330400-40331000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
24	chr15:40330400-40331000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
25	chr15:40330400-40331000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr15:40330400-40331000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr15:40330400-40331200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
28	chr15:40330400-40331600	Active TSS	H1 Cell Line	embryonic stem cell
29	chr15:40330400-40331600	Active TSS	iPS-20b Cell Line	embryonic stem cell
30	chr15:40330400-40331600	Active TSS	Brain Angular Gyrus	brain
31	chr15:40330400-40331600	Active TSS	Osteobl	bone
32	chr15:40330400-40331800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr15:40330400-40331800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr15:40330400-40331800	Active TSS	Aorta	Aorta
35	chr15:40330400-40331800	Active TSS	Brain Hippocampus Middle	brain
36	chr15:40330400-40331800	Active TSS	Fetal Brain Female	brain
37	chr15:40330400-40331800	Active TSS	Fetal Muscle Trunk	muscle
38	chr15:40330400-40331800	Active TSS	Placenta Amnion	Placenta Amnion
39	chr15:40330400-40331800	Bivalent/Poised TSS	HepG2	liver
40	chr15:40330400-40332000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr15:40330400-40332000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr15:40330400-40332000	Active TSS	HUES48 Cell Line	embryonic stem cell
43	chr15:40330400-40332000	Active TSS	HUES6 Cell Line	embryonic stem cell
44	chr15:40330400-40332000	Active TSS	iPS-15b Cell Line	embryonic stem cell
45	chr15:40330400-40332000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr15:40330400-40332000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr15:40330400-40332000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr15:40330400-40332000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr15:40330400-40332000	Active TSS	Esophagus	oesophagus
50	chr15:40330400-40332000	Active TSS	Fetal Intestine Small	intestine

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