Variant report

Variant	rs2277458
Chromosome Location	chr14:39583481-39583482
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:312)
CpG islands
(count:61)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:312 , 50 per page) page: 1 2 3 4 5 6 7

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NRF1	chr14:39583191-39583707	H1-hESC	embryonic stem cell:	n/a	chr14:39583477-39583491 chr14:39583504-39583515 chr14:39583480-39583491 chr14:39583480-39583494
2	POLR2A	chr14:39583214-39583853	HL-60	blood:	n/a	n/a
3	POLR2A	chr14:39582984-39583954	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr14:39583304-39583840	GM12878	blood:	n/a	n/a
5	YY1	chr14:39583280-39583747	SK-N-SH_RA	brain:	n/a	chr14:39583716-39583727
6	POU2F2	chr14:39583196-39583848	GM12878	blood:	n/a	n/a
7	POLR2A	chr14:39583057-39583839	PANC-1	pancreas:	n/a	n/a
8	REST	chr14:39583297-39583731	PFSK-1	brain:	n/a	n/a
9	MAFK	chr14:39583233-39583853	HepG2	liver:	n/a	n/a
10	POLR2A	chr14:39583336-39583696	A549	lung:	n/a	n/a
11	POLR2A	chr14:39583098-39583795	SK-N-MC	brain:	n/a	n/a
12	TAF1	chr14:39583285-39583832	HepG2	liver:	n/a	n/a
13	FOS	chr14:39583175-39583572	MCF10A-Er-Src	breast:	n/a	n/a
14	POLR2A	chr14:39583212-39583836	GM18526	blood:	n/a	n/a
15	TAF1	chr14:39583267-39583699	SK-N-SH	brain:	n/a	n/a
16	ARID3A	chr14:39582908-39583545	K562	blood:	n/a	n/a
17	E2F6	chr14:39583021-39583734	A549	lung:	n/a	chr14:39583481-39583490
18	POLR2A	chr14:39583198-39583851	GM12891	blood:	n/a	n/a
19	MYC	chr14:39583242-39583803	K562	blood:	n/a	n/a
20	TAF1	chr14:39583271-39583669	K562	blood:	n/a	n/a
21	POLR2A	chr14:39583259-39583828	HepG2	liver:	n/a	n/a
22	MYC	chr14:39583226-39584024	MCF10A-Er-Src	breast:	n/a	n/a
23	CEBPB	chr14:39583223-39583559	A549	lung:	n/a	n/a
24	USF1	chr14:39583171-39583668	A549	lung:	n/a	n/a
25	YY1	chr14:39583221-39583695	HCT-116	colon:	n/a	n/a
26	FOXA2	chr14:39583144-39583945	HepG2	liver:	n/a	n/a
27	MAZ	chr14:39583125-39583928	Hela-S3	cervix:	n/a	n/a
28	RUNX3	chr14:39583187-39583761	GM12878	blood:	n/a	n/a
29	YY1	chr14:39583333-39583729	GM12891	blood:	n/a	chr14:39583716-39583727
30	TAF1	chr14:39583082-39583914	ECC-1	luminal epithelium:	n/a	n/a
31	POLR2A	chr14:39583265-39583851	HepG2	liver:	n/a	n/a
32	CTCF	chr14:39583429-39583632	K562	blood:	n/a	n/a
33	REST	chr14:39582923-39584191	H1-neurons	neurons:	n/a	n/a
34	POLR2A	chr14:39583135-39583757	U87	brain:	n/a	n/a
35	RAD21	chr14:39583402-39583767	HepG2	liver:	n/a	n/a
36	POLR2A	chr14:39583278-39583760	A549	lung:	n/a	n/a
37	POLR2A	chr14:39583345-39583786	A549	lung:	n/a	n/a
38	RCOR1	chr14:39583143-39583903	Hela-S3	cervix:	n/a	n/a
39	SIN3A	chr14:39583323-39583987	H1-hESC	embryonic stem cell:	n/a	n/a
40	TAF1	chr14:39583235-39583852	HepG2	liver:	n/a	n/a
41	RCOR1	chr14:39583399-39584211	K562	blood:	n/a	n/a
42	NFIC	chr14:39583101-39584260	HepG2	liver:	n/a	n/a
43	ELF1	chr14:39583219-39583802	GM12878	blood:	n/a	n/a
44	YY1	chr14:39583311-39583721	K562	blood:	n/a	n/a
45	REST	chr14:39583017-39583781	HL-60	blood:	n/a	n/a
46	FOXP2	chr14:39583298-39583596	SK-N-MC	brain:	n/a	n/a
47	CEBPB	chr14:39583219-39584060	A549	lung:	n/a	n/a
48	POLR2A	chr14:39583125-39583856	NB4	blood:	n/a	n/a
49	TAF1	chr14:39583109-39583925	A549	lung:	n/a	n/a
50	TAF1	chr14:39583291-39583825	K562	blood:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr14:39583459-39583509	PFSK-1	brain:	n/a
2	chr14:39583459-39583509	Hela-S3	cervix:	n/a
3	chr14:39583459-39583509	SAEC	small airway:	n/a
4	chr14:39583459-39583509	HPAEpiC	pulmonary alveolar:	n/a
5	chr14:39583459-39583509	HIPEpiC	eye:	n/a
6	chr14:39583459-39583509	NT2-D1	testis:	n/a
7	chr14:39583459-39583509	HEK293	kidney:	embryo
8	chr14:39583459-39583509	HAEpiC	amniotic membrane:	n/a
9	chr14:39583459-39583509	HEEpiC	esophagus:	n/a
10	chr14:39583459-39583509	AG10803	skin:	n/a
11	chr14:39583459-39583509	HRPEpiC	eye:	n/a
12	chr14:39583459-39583509	MCF10A-Er-Src	breast:	n/a
13	chr14:39583459-39583509	Jurkat	blood:	n/a
14	chr14:39583459-39583509	PrEC	prostate:	n/a
15	chr14:39583459-39583509	HCF	heart:	n/a
16	chr14:39583459-39583509	BE2_C	brain:	n/a
17	chr14:39583459-39583509	HL-60	blood:	n/a
18	chr14:39583459-39583509	K562	blood:	n/a
19	chr14:39583459-39583509	NB4	blood:	n/a
20	chr14:39583459-39583509	HRE	kidney:	n/a
21	chr14:39583459-39583509	GM12891	blood:	n/a
22	chr14:39583459-39583509	HCM	heart:	n/a
23	chr14:39583459-39583509	NHBE	bronchial:	n/a
24	chr14:39583459-39583509	BJ	skin:	n/a
25	chr14:39583459-39583509	ProgFib	skin:	n/a
26	chr14:39583459-39583509	AG09309	skin:	n/a
27	chr14:39583459-39583509	U87	brain:	n/a
28	chr14:39583459-39583509	RPTEC	kidney:	n/a
29	chr14:39583459-39583509	SK-N-SH_RA	brain:	n/a
30	chr14:39583459-39583509	AoSMC	blood vessel:	n/a
31	chr14:39583459-39583509	ECC-1	luminal epithelium:	n/a
32	chr14:39583459-39583509	CMK	blood:	n/a
33	chr14:39583459-39583509	HNPCEpiC	eye:	n/a
34	chr14:39583459-39583509	GM06990	blood:	n/a
35	chr14:39583459-39583509	HCPEpiC	choroid plexus:	n/a
36	chr14:39583459-39583509	Hepatocyte	liver:	n/a
37	chr14:39583459-39583509	GM12892	blood:	n/a
38	chr14:39583459-39583509	HMEC	breast:	n/a
39	chr14:39583459-39583509	HRCEpiC	kidney:	n/a
40	chr14:39583459-39583509	SKMC	muscle:	n/a
41	chr14:39583459-39583509	SK-N-MC	brain:	n/a
42	chr14:39583459-39583509	AG04450	lung:	fetal
43	chr14:39583459-39583509	HCT-116	colon:	n/a
44	chr14:39583459-39583509	AG04449	skin:	fetal
45	chr14:39583459-39583509	MCF-7	breast:	n/a
46	chr14:39583459-39583509	PANC-1	pancreas:	n/a
47	chr14:39583459-39583509	T-47D	breast:	n/a
48	chr14:39583459-39583509	IMR90	lung:	fetal
49	chr14:39583459-39583509	NHDF-neo	bronchial:	n/a
50	chr14:39583459-39583509	NH-A	brain:	n/a

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr14:39583285..39585580-chr14:39639274..39641168,2	K562	blood:
2	chr14:39582528..39584759-chr14:39643385..39645029,2	K562	blood:
3	chr14:39582116..39585012-chr14:39643452..39645860,4	MCF-7	breast:
4	chr14:39582047..39584964-chr14:39643383..39645099,4	K562	blood:
5	chr14:39582622..39586619-chr14:39638047..39642701,6	MCF-7	breast:
6	chr14:39581660..39583614-chr5:118323067..118325473,2	MCF-7	breast:
7	chr14:39572488..39573108-chr14:39583111..39583768,2	HCT-116	colon:

No data

Variant related genes	Relation type
SEC23A	TF binding region
GEMIN2	TF binding region
GEMIN2	CpG island
SEC23A	CpG island
ENSG00000100934	Chromatin interaction
ENSG00000259083	Chromatin interaction
ENSG00000169570	Chromatin interaction
ENSG00000100941	Chromatin interaction
ENSG00000182400	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1002193	0.90[CHB][hapmap];0.85[JPT][hapmap]
rs10131369	0.90[CHB][hapmap];0.91[JPT][hapmap]
rs10134166	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs10135561	0.90[CHB][hapmap];0.91[JPT][hapmap]
rs10140763	0.80[ASN][1000 genomes]
rs10141924	0.90[CHB][hapmap];0.91[JPT][hapmap]
rs10148712	0.90[CHB][hapmap];0.91[JPT][hapmap]
rs1050136	0.90[CHB][hapmap];0.91[JPT][hapmap]
rs11622731	0.90[CHB][hapmap];0.91[JPT][hapmap]
rs11626002	0.90[CHB][hapmap];0.91[JPT][hapmap]
rs11849209	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs12587208	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs13021	0.90[CHB][hapmap];0.91[JPT][hapmap]
rs17092044	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs17092050	0.81[ASN][1000 genomes]
rs1884384	1.00[ASW][hapmap];0.91[CEU][hapmap];0.81[GIH][hapmap];0.86[LWK][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap];0.91[YRI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2144529	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2144530	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2180216	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2273592	0.85[CHB][hapmap];0.91[JPT][hapmap]
rs3818163	0.82[JPT][hapmap]
rs7156264	0.80[CHB][hapmap]
rs8014813	0.82[JPT][hapmap]
rs8018720	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8022510	0.92[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]

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	esv3429206	chr14:39160730-39648836	Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv1038622	chr14:39423562-39604035	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2277458	SIP1	cis	parietal	SCAN
rs2277458	EAPP	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:39581800-39584200	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr14:39582400-39584200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
3	chr14:39582400-39584400	Active TSS	H1 Cell Line	embryonic stem cell
4	chr14:39582400-39584400	Active TSS	A549	lung
5	chr14:39582400-39584600	Active TSS	HUES6 Cell Line	embryonic stem cell
6	chr14:39582800-39584000	Active TSS	Brain Hippocampus Middle	brain
7	chr14:39582800-39584000	Active TSS	Brain Inferior Temporal Lobe	brain
8	chr14:39582800-39584000	Active TSS	Brain Substantia Nigra	brain
9	chr14:39582800-39584000	Active TSS	Rectal Mucosa Donor 29	rectum
10	chr14:39582800-39584200	Active TSS	Colon Smooth Muscle	Colon
11	chr14:39582800-39584600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr14:39582800-39584600	Active TSS	Pancreatic Islets	Pancreatic Islet
13	chr14:39583000-39583600	Active TSS	Duodenum Mucosa	Duodenum
14	chr14:39583000-39583600	Active TSS	Skeletal Muscle Female	skeletal muscle
15	chr14:39583000-39583800	Active TSS	Primary T cells from cord blood	blood
16	chr14:39583000-39583800	Active TSS	Rectal Mucosa Donor 31	rectum
17	chr14:39583000-39584000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr14:39583000-39584000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr14:39583000-39584000	Active TSS	Aorta	Aorta
20	chr14:39583000-39584000	Active TSS	Brain Angular Gyrus	brain
21	chr14:39583000-39584000	Active TSS	Brain Anterior Caudate	brain
22	chr14:39583000-39584000	Active TSS	Brain Cingulate Gyrus	brain
23	chr14:39583000-39584000	Active TSS	Brain Germinal Matrix	brain
24	chr14:39583000-39584000	Active TSS	Fetal Adrenal Gland	Adrenal Gland
25	chr14:39583000-39584000	Active TSS	Fetal Brain Female	brain
26	chr14:39583000-39584000	Active TSS	Fetal Intestine Large	intestine
27	chr14:39583000-39584000	Active TSS	Fetal Muscle Leg	muscle
28	chr14:39583000-39584000	Active TSS	Fetal Stomach	stomach
29	chr14:39583000-39584000	Active TSS	Skeletal Muscle Male	skeletal muscle
30	chr14:39583000-39584000	Active TSS	Thymus	Thymus
31	chr14:39583000-39584000	Active TSS	Osteobl	bone
32	chr14:39583000-39584200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr14:39583000-39584200	Active TSS	Breast Myoepithelial Primary Cells	Breast
34	chr14:39583000-39584200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
35	chr14:39583000-39584200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
36	chr14:39583000-39584200	Active TSS	Fetal Kidney	kidney
37	chr14:39583000-39584200	Active TSS	Ovary	ovary
38	chr14:39583000-39584200	Active TSS	Hela-S3	cervix
39	chr14:39583000-39584200	Active TSS	HMEC	breast
40	chr14:39583000-39584400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr14:39583000-39584400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr14:39583000-39584400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr14:39583000-39584400	Flanking Active TSS	Primary hematopoietic stem cells	blood
44	chr14:39583000-39584400	Flanking Active TSS	Adipose Nuclei	Adipose
45	chr14:39583000-39584400	Active TSS	Psoas Muscle	Psoas
46	chr14:39583000-39584400	Active TSS	Right Atrium	heart
47	chr14:39583000-39584400	Active TSS	NHLF	lung
48	chr14:39583000-39584600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr14:39583000-39584600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr14:39583000-39584600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin

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