Variant report

Variant	rs512458
Chromosome Location	chr1:212588893-212588894
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:51)
CpG islands
(count:61)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:51 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MYC	chr1:212587629-212589222	NB4	blood:	n/a	chr1:212588309-212588319 chr1:212587669-212587679
2	TEAD4	chr1:212588004-212589288	K562	blood:	n/a	n/a
3	CHD2	chr1:212588043-212589141	GM12878	blood:	n/a	n/a
4	MAX	chr1:212587315-212589069	GM12878	blood:	n/a	chr1:212588309-212588319 chr1:212587669-212587679
5	NFIC	chr1:212588085-212589257	GM12878	blood:	n/a	n/a
6	HCFC1	chr1:212587426-212589189	K562	blood:	n/a	n/a
7	POLR2A	chr1:212587484-212589250	GM12878	blood:	n/a	n/a
8	POLR2A	chr1:212587954-212589321	HL-60	blood:	n/a	n/a
9	SREBP1	chr1:212587176-212589923	GM12878	blood:	n/a	n/a
10	WRNIP1	chr1:212588225-212589185	GM12878	blood:	n/a	n/a
11	CEBPB	chr1:212588000-212589247	GM12878	blood:	n/a	n/a
12	CBX3	chr1:212587912-212589221	K562	blood:	n/a	n/a
13	TCF12	chr1:212588853-212589148	GM12878	blood:	n/a	n/a
14	POLR2A	chr1:212587655-212589175	GM19193	blood:	n/a	n/a
15	POU2F2	chr1:212588729-212589262	GM12878	blood:	n/a	n/a
16	NFATC1	chr1:212587990-212589147	GM12878	blood:	n/a	n/a
17	BHLHE40	chr1:212588036-212589170	K562	blood:	n/a	chr1:212588255-212588271
18	TCF12	chr1:212588837-212589223	GM12878	blood:	n/a	n/a
19	MAX	chr1:212587427-212589193	NB4	blood:	n/a	chr1:212588309-212588319 chr1:212587669-212587679
20	ZC3H11A	chr1:212588816-212589057	K562	blood:	n/a	n/a
21	JUN	chr1:212586575-212589515	K562	blood:	n/a	chr1:212587985-212587994 chr1:212589466-212589475
22	FOXM1	chr1:212588738-212589362	GM12878	blood:	n/a	n/a
23	POLR2A	chr1:212587788-212589160	GM12891	blood:	n/a	n/a
24	FOXM1	chr1:212587882-212589328	GM12878	blood:	n/a	n/a
25	HCFC1	chr1:212586968-212588965	Hela-S3	cervix:	n/a	n/a
26	POLR2A	chr1:212587494-212589159	GM12892	blood:	n/a	n/a
27	POLR2A	chr1:212587768-212589166	NB4	blood:	n/a	n/a
28	POLR2A	chr1:212587821-212589244	GM12878	blood:	n/a	n/a
29	STAT5A	chr1:212587685-212589154	GM12878	blood:	n/a	n/a
30	RUNX3	chr1:212587429-212589362	GM12878	blood:	n/a	n/a
31	NR2F2	chr1:212587571-212589354	K562	blood:	n/a	n/a
32	ZNF143	chr1:212588058-212589043	K562	blood:	n/a	chr1:212588298-212588307 chr1:212588296-212588305
33	POLR2A	chr1:212588077-212589029	PBDE	blood:	n/a	n/a
34	RELA	chr1:212588214-212589036	GM19099	blood:	n/a	n/a
35	REST	chr1:212588148-212589271	HL-60	blood:	n/a	n/a
36	ATF2	chr1:212588062-212588986	GM12878	blood:	n/a	n/a
37	SPI1	chr1:212587991-212589166	HL-60	blood:	n/a	chr1:212588413-212588426 chr1:212588507-212588516 chr1:212588508-212588515 chr1:212588414-212588427 chr1:212588416-212588423 chr1:212588411-212588420 chr1:212589026-212589033
38	MTA3	chr1:212586945-212589216	GM12878	blood:	n/a	n/a
39	POLR2A	chr1:212588882-212589184	GM12878	blood:	n/a	n/a
40	SPI1	chr1:212587811-212588947	GM12878	blood:	n/a	chr1:212588413-212588426 chr1:212588507-212588516 chr1:212588508-212588515 chr1:212588414-212588427 chr1:212588416-212588423 chr1:212588411-212588420
41	BHLHE40	chr1:212588069-212589066	GM12878	blood:	n/a	chr1:212588255-212588271
42	POLR2A	chr1:212587926-212589092	GM12878	blood:	n/a	n/a
43	POLR2A	chr1:212587790-212589312	GM12892	blood:	n/a	n/a
44	RUNX3	chr1:212587943-212589414	GM12878	blood:	n/a	n/a
45	MAFK	chr1:212588235-212589013	K562	blood:	n/a	n/a
46	POLR2A	chr1:212587692-212589164	GM18505	blood:	n/a	n/a
47	POLR2A	chr1:212587754-212589151	GM19099	blood:	n/a	n/a
48	EBF1	chr1:212588802-212589220	GM12878	blood:	n/a	n/a
49	PML	chr1:212587587-212589140	GM12878	blood:	n/a	chr1:212587706-212587714 chr1:212588920-212588928
50	CHD1	chr1:212587999-212588986	GM12878	blood:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:212588848-212588898	H1-hESC	embryonic stem cell:	embryo
2	chr1:212588848-212588898	NH-A	brain:	n/a
3	chr1:212588848-212588898	BE2_C	brain:	n/a
4	chr1:212588848-212588898	SK-N-SH	brain:	n/a
5	chr1:212588848-212588898	RPTEC	kidney:	n/a
6	chr1:212588848-212588898	PrEC	prostate:	n/a
7	chr1:212588848-212588898	HepG2	liver:	n/a
8	chr1:212588848-212588898	PANC-1	pancreas:	n/a
9	chr1:212588848-212588898	AG09319	gingival:	n/a
10	chr1:212588848-212588898	SK-N-MC	brain:	n/a
11	chr1:212588848-212588898	HRE	kidney:	n/a
12	chr1:212588848-212588898	K562	blood:	n/a
13	chr1:212588848-212588898	T-47D	breast:	n/a
14	chr1:212588848-212588898	NHBE	bronchial:	n/a
15	chr1:212588848-212588898	SKMC	muscle:	n/a
16	chr1:212588848-212588898	HL-60	blood:	n/a
17	chr1:212588848-212588898	HEEpiC	esophagus:	n/a
18	chr1:212588848-212588898	HPAEpiC	pulmonary alveolar:	n/a
19	chr1:212588848-212588898	AoSMC	blood vessel:	n/a
20	chr1:212588848-212588898	SK-N-SH_RA	brain:	n/a
21	chr1:212588848-212588898	HCF	heart:	n/a
22	chr1:212588848-212588898	BJ	skin:	n/a
23	chr1:212588848-212588898	GM19239	blood:	n/a
24	chr1:212588848-212588898	AG10803	skin:	n/a
25	chr1:212588848-212588898	HAEpiC	amniotic membrane:	n/a
26	chr1:212588848-212588898	GM12891	blood:	n/a
27	chr1:212588848-212588898	Hepatocyte	liver:	n/a
28	chr1:212588848-212588898	ovcar-3	ovarian:	n/a
29	chr1:212588848-212588898	NT2-D1	testis:	n/a
30	chr1:212588848-212588898	HIPEpiC	eye:	n/a
31	chr1:212588848-212588898	A549	lung:	n/a
32	chr1:212588848-212588898	AG09309	skin:	n/a
33	chr1:212588848-212588898	Hela-S3	cervix:	n/a
34	chr1:212588848-212588898	HCT-116	colon:	n/a
35	chr1:212588848-212588898	IMR90	lung:	fetal
36	chr1:212588848-212588898	HCM	heart:	n/a
37	chr1:212588848-212588898	HRPEpiC	eye:	n/a
38	chr1:212588848-212588898	Jurkat	blood:	n/a
39	chr1:212588848-212588898	AG04449	skin:	fetal
40	chr1:212588848-212588898	HMEC	breast:	n/a
41	chr1:212588848-212588898	NHDF-neo	bronchial:	n/a
42	chr1:212588848-212588898	GM12878	blood:	n/a
43	chr1:212588848-212588898	HNPCEpiC	eye:	n/a
44	chr1:212588848-212588898	HEK293	kidney:	embryo
45	chr1:212588848-212588898	GM06990	blood:	n/a
46	chr1:212588848-212588898	HCPEpiC	choroid plexus:	n/a
47	chr1:212588848-212588898	ProgFib	skin:	n/a
48	chr1:212588848-212588898	AG04450	lung:	fetal
49	chr1:212588848-212588898	SAEC	small airway:	n/a
50	chr1:212588848-212588898	Caco-2	colon:	n/a

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:212588338..212589858-chr1:212645243..212647080,2	K562	blood:
2	chr1:212587143..212589756-chr1:212965630..212967810,2	K562	blood:
3	chr1:212586222..212588940-chr1:212781343..212783037,2	K562	blood:
4	chr1:212586060..212592297-chr1:212603893..212609565,9	MCF-7	breast:
5	chr1:212588056..212590074-chr1:212779163..212783567,3	K562	blood:
6	chr1:212549233..212551182-chr1:212586836..212589324,2	K562	blood:
7	chr1:212587912..212590110-chr1:212604889..212609190,4	K562	blood:
8	chr1:212585974..212594847-chr1:212598812..212609579,19	K562	blood:
9	chr1:212581574..212584496-chr1:212586803..212589409,2	MCF-7	breast:

No data

Variant related genes	Relation type
TMEM206	TF binding region
TMEM206	CpG island
ENSG00000117691	Chromatin interaction
ENSG00000162772	Chromatin interaction
ENSG00000065600	Chromatin interaction
ENSG00000203705	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs1086892	0.83[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009376	chr1:212292357-212680320	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv549139	chr1:212332294-212876902	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
3	nsv997629	chr1:212404489-212658785	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv535286	chr1:212404489-212658785	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
5	nsv1013110	chr1:212555764-212948092	Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
6	nsv535287	chr1:212555764-212948092	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
7	esv1828436	chr1:212577765-212591863	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
8	nsv873156	chr1:212585092-212646225	Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs512458	IL24	cis	cerebellum	SCAN
rs512458	C4BPA	cis	cerebellum	SCAN
rs512458	PROX1	cis	parietal	SCAN

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212587000-212589000	Active TSS	Rectal Smooth Muscle	rectum
2	chr1:212587400-212589000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr1:212587800-212589000	Active TSS	Stomach Smooth Muscle	stomach
4	chr1:212588200-212589000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
5	chr1:212588200-212589000	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
6	chr1:212588200-212589000	Flanking Active TSS	Brain Substantia Nigra	brain
7	chr1:212588200-212589000	Flanking Active TSS	Dnd41	blood
8	chr1:212588200-212589200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
9	chr1:212588400-212589000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr1:212588400-212589000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr1:212588400-212589000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
12	chr1:212588400-212589000	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr1:212588400-212589000	Flanking Active TSS	Brain Anterior Caudate	brain
14	chr1:212588400-212589000	Flanking Active TSS	Brain Cingulate Gyrus	brain
15	chr1:212588400-212589000	Flanking Active TSS	Brain Hippocampus Middle	brain
16	chr1:212588400-212589000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
17	chr1:212588400-212589000	Flanking Active TSS	K562	blood
18	chr1:212588400-212589200	Enhancers	H1 Cell Line	embryonic stem cell
19	chr1:212588400-212589200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr1:212588400-212589200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr1:212588400-212589200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr1:212588400-212589200	Enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr1:212588400-212589200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr1:212588400-212589200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr1:212588400-212589200	Flanking Active TSS	HepG2	liver
26	chr1:212588400-212589200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
27	chr1:212588400-212589400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr1:212588400-212590200	Enhancers	Primary hematopoietic stem cells	blood
29	chr1:212588400-212590600	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr1:212588600-212589000	Enhancers	iPS-15b Cell Line	embryonic stem cell
31	chr1:212588600-212589000	Enhancers	iPS-18 Cell Line	embryonic stem cell
32	chr1:212588600-212589000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
33	chr1:212588600-212589000	Enhancers	Primary T helper cells PMA-I stimulated	--
34	chr1:212588600-212589000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr1:212588600-212589000	Enhancers	Fetal Intestine Small	intestine
36	chr1:212588600-212589000	Enhancers	Sigmoid Colon	Sigmoid Colon
37	chr1:212588600-212589000	Enhancers	HUVEC	blood vessel
38	chr1:212588600-212589200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr1:212588600-212589200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr1:212588600-212589200	Enhancers	HUES48 Cell Line	embryonic stem cell
41	chr1:212588600-212589200	Enhancers	HUES6 Cell Line	embryonic stem cell
42	chr1:212588600-212589200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr1:212588600-212589200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr1:212588600-212589200	Enhancers	Primary T cells fromperipheralblood	blood
45	chr1:212588600-212589200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
46	chr1:212588600-212589200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
47	chr1:212588600-212589200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr1:212588600-212589200	Enhancers	Fetal Muscle Trunk	muscle
49	chr1:212588600-212589200	Enhancers	Fetal Muscle Leg	muscle
50	chr1:212588600-212589200	Enhancers	Placenta	Placenta

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