Variant report

Variant	rs12432098
Chromosome Location	chr14:31090558-31090559
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:127)
CpG islands
(count:61)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr14:31090546-31090928	A549	lung:	n/a	n/a
2	POLR2A	chr14:31090434-31092076	H1-hESC	embryonic stem cell:	n/a	n/a
3	MAX	chr14:31090243-31091996	MCF-7	breast:	n/a	chr14:31090438-31090446 chr14:31090435-31090444 chr14:31090433-31090446 chr14:31090435-31090444 chr14:31090434-31090445
4	NR2F2	chr14:31090464-31092008	MCF-7	breast:	n/a	n/a
5	POLR2A	chr14:31090359-31092144	GM12878	blood:	n/a	n/a
6	POLR2A	chr14:31090392-31091954	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr14:31090525-31090921	GM12878	blood:	n/a	n/a
8	POLR2A	chr14:31090527-31091944	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr14:31090445-31092145	H1-hESC	embryonic stem cell:	n/a	n/a
10	MBD4	chr14:31090107-31092432	HepG2	liver:	n/a	n/a
11	POLR2A	chr14:31090556-31090955	SK-N-SH	brain:	n/a	n/a
12	POLR2A	chr14:31090363-31092065	GM12878	blood:	n/a	n/a
13	MTA3	chr14:31090324-31092061	GM12878	blood:	n/a	n/a
14	GATA3	chr14:31090227-31092177	MCF-7	breast:	n/a	chr14:31091901-31091908 chr14:31091901-31091908 chr14:31091897-31091913 chr14:31091901-31091908 chr14:31091894-31091915
15	POLR2A	chr14:31090470-31092023	GM12891	blood:	n/a	n/a
16	POLR2A	chr14:31090488-31092093	HUVEC	blood vessel:	n/a	n/a
17	TCF12	chr14:31090529-31092054	A549	lung:	n/a	n/a
18	POLR2A	chr14:31090321-31092018	GM18505	blood:	n/a	n/a
19	POLR2A	chr14:31090367-31092021	SK-N-SH	brain:	n/a	n/a
20	POLR2A	chr14:31090496-31092001	K562	blood:	n/a	n/a
21	POLR2A	chr14:31090449-31092032	GM12891	blood:	n/a	n/a
22	POLR2A	chr14:31090537-31090898	MCF-7	breast:	n/a	n/a
23	USF1	chr14:31090299-31090670	SK-N-SH_RA	brain:	n/a	chr14:31090433-31090444
24	POLR2A	chr14:31090464-31091948	HepG2	liver:	n/a	n/a
25	TAF1	chr14:31090525-31092001	MCF-7	breast:	n/a	n/a
26	POLR2A	chr14:31090323-31091871	PANC-1	pancreas:	n/a	n/a
27	POLR2A	chr14:31090538-31092149	HUVEC	blood vessel:	n/a	n/a
28	POLR2A	chr14:31090528-31091927	HepG2	liver:	n/a	n/a
29	BCL3	chr14:31090258-31092000	A549	lung:	n/a	n/a
30	POLR2A	chr14:31090356-31091031	K562	blood:	n/a	n/a
31	YY1	chr14:31090495-31090842	K562	blood:	n/a	n/a
32	BCL3	chr14:31090411-31092048	A549	lung:	n/a	n/a
33	ATF2	chr14:31090487-31092090	GM12878	blood:	n/a	n/a
34	JUND	chr14:31090300-31091970	MCF-7	breast:	n/a	chr14:31091146-31091155 chr14:31091453-31091467 chr14:31091951-31091965
35	POLR2A	chr14:31090415-31092079	K562	blood:	n/a	n/a
36	ZNF384	chr14:31090396-31091623	K562	blood:	n/a	n/a
37	USF1	chr14:31090266-31090645	K562	blood:	n/a	chr14:31090433-31090444
38	FOSL2	chr14:31090465-31091866	MCF-7	breast:	n/a	chr14:31091146-31091155 chr14:31091453-31091467
39	NFATC1	chr14:31090365-31091994	GM12878	blood:	n/a	n/a
40	POLR2A	chr14:31090344-31092059	HepG2	liver:	n/a	n/a
41	ELF1	chr14:31090391-31091983	MCF-7	breast:	n/a	chr14:31091499-31091511 chr14:31091454-31091465
42	POLR2A	chr14:31090446-31092051	K562	blood:	n/a	n/a
43	POLR2A	chr14:31090337-31092113	SK-N-MC	brain:	n/a	n/a
44	ELF1	chr14:31090419-31092132	MCF-7	breast:	n/a	chr14:31091499-31091511 chr14:31091454-31091465
45	POLR2A	chr14:31090463-31092011	ECC-1	luminal epithelium:	n/a	n/a
46	POLR2A	chr14:31090508-31092060	GM12892	blood:	n/a	n/a
47	ELF1	chr14:31090522-31091007	HepG2	liver:	n/a	n/a
48	POLR2A	chr14:31090544-31091995	GM18951	blood:	n/a	n/a
49	POLR2A	chr14:31090409-31092098	PFSK-1	brain:	n/a	n/a
50	RELA	chr14:31090553-31092021	GM19099	blood:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr14:31090535-31090585	SK-N-SH_RA	brain:	n/a
2	chr14:31090535-31090585	HEK293	kidney:	embryo
3	chr14:31090535-31090585	AG10803	skin:	n/a
4	chr14:31090535-31090585	SAEC	small airway:	n/a
5	chr14:31090535-31090585	HepG2	liver:	n/a
6	chr14:31090535-31090585	HRPEpiC	eye:	n/a
7	chr14:31090535-31090585	H1-hESC	embryonic stem cell:	embryo
8	chr14:31090535-31090585	HCF	heart:	n/a
9	chr14:31090535-31090585	NH-A	brain:	n/a
10	chr14:31090535-31090585	NHBE	bronchial:	n/a
11	chr14:31090535-31090585	AG04449	skin:	fetal
12	chr14:31090535-31090585	NHDF-neo	bronchial:	n/a
13	chr14:31090535-31090585	PFSK-1	brain:	n/a
14	chr14:31090535-31090585	SKMC	muscle:	n/a
15	chr14:31090535-31090585	HCPEpiC	choroid plexus:	n/a
16	chr14:31090535-31090585	HIPEpiC	eye:	n/a
17	chr14:31090535-31090585	HPAEpiC	pulmonary alveolar:	n/a
18	chr14:31090535-31090585	SK-N-MC	brain:	n/a
19	chr14:31090535-31090585	A549	lung:	n/a
20	chr14:31090535-31090585	NT2-D1	testis:	n/a
21	chr14:31090535-31090585	SK-N-SH	brain:	n/a
22	chr14:31090535-31090585	Caco-2	colon:	n/a
23	chr14:31090535-31090585	LNCaP	prostate:	n/a
24	chr14:31090535-31090585	AG04450	lung:	fetal
25	chr14:31090535-31090585	HL-60	blood:	n/a
26	chr14:31090535-31090585	MCF-7	breast:	n/a
27	chr14:31090535-31090585	ovcar-3	ovarian:	n/a
28	chr14:31090535-31090585	BJ	skin:	n/a
29	chr14:31090535-31090585	PrEC	prostate:	n/a
30	chr14:31090535-31090585	U87	brain:	n/a
31	chr14:31090535-31090585	GM12892	blood:	n/a
32	chr14:31090535-31090585	IMR90	lung:	fetal
33	chr14:31090535-31090585	GM19239	blood:	n/a
34	chr14:31090535-31090585	GM06990	blood:	n/a
35	chr14:31090535-31090585	NB4	blood:	n/a
36	chr14:31090535-31090585	MCF10A-Er-Src	breast:	n/a
37	chr14:31090535-31090585	GM12878	blood:	n/a
38	chr14:31090535-31090585	HCM	heart:	n/a
39	chr14:31090535-31090585	BE2_C	brain:	n/a
40	chr14:31090535-31090585	HRCEpiC	kidney:	n/a
41	chr14:31090535-31090585	Jurkat	blood:	n/a
42	chr14:31090535-31090585	CMK	blood:	n/a
43	chr14:31090535-31090585	PANC-1	pancreas:	n/a
44	chr14:31090535-31090585	HMEC	breast:	n/a
45	chr14:31090535-31090585	AoSMC	blood vessel:	n/a
46	chr14:31090535-31090585	Hepatocyte	liver:	n/a
47	chr14:31090535-31090585	GM12891	blood:	n/a
48	chr14:31090535-31090585	ProgFib	skin:	n/a
49	chr14:31090535-31090585	ECC-1	luminal epithelium:	n/a
50	chr14:31090535-31090585	HEEpiC	esophagus:	n/a

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr14:31090296..31092019-chr14:31343870..31346650,2	K562	blood:
2	chr14:31090018..31093014-chr14:31887951..31890191,2	MCF-7	breast:
3	chr14:31090029..31096005-chr14:31342159..31346650,8	K562	blood:
4	chr14:31090421..31092379-chr14:31107832..31110754,2	MCF-7	breast:
5	chr14:31027121..31031753-chr14:31090278..31094067,6	K562	blood:
6	chr14:31060440..31063351-chr14:31089762..31092777,3	MCF-7	breast:
7	chr14:31074562..31083390-chr14:31084587..31093565,15	K562	blood:
8	chr14:31071248..31073927-chr14:31089916..31091588,2	MCF-7	breast:
9	chr14:31067708..31069634-chr14:31090291..31092583,3	MCF-7	breast:
10	chr14:31025231..31028884-chr14:31089510..31093231,4	MCF-7	breast:
11	chr14:31027330..31031100-chr14:31087785..31093139,9	MCF-7	breast:

No data

Variant related genes	Relation type
SCFD1	TF binding region
SCFD1	CpG island
ENSG00000129493	Chromatin interaction
ENSG00000092108	Chromatin interaction
ENSG00000250365	Chromatin interaction
ENSG00000092140	Chromatin interaction
ENSG00000100473	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10130830	1.00[YRI][hapmap]
rs10142331	1.00[YRI][hapmap]
rs11625381	1.00[YRI][hapmap]
rs11846420	1.00[YRI][hapmap]
rs12434151	1.00[YRI][hapmap]
rs12434610	0.81[EUR][1000 genomes]
rs151123	1.00[YRI][hapmap]
rs172946	1.00[YRI][hapmap]
rs2070339	1.00[YRI][hapmap]
rs229144	1.00[YRI][hapmap]
rs229152	1.00[YRI][hapmap]
rs229154	1.00[YRI][hapmap]
rs229161	1.00[YRI][hapmap]
rs229179	1.00[YRI][hapmap]
rs229184	1.00[YRI][hapmap]
rs229201	1.00[YRI][hapmap]
rs229211	1.00[YRI][hapmap]
rs229237	0.85[YRI][hapmap]
rs230351	1.00[YRI][hapmap]
rs230364	1.00[YRI][hapmap]
rs230366	1.00[YRI][hapmap]
rs2378782	1.00[YRI][hapmap]
rs448175	1.00[YRI][hapmap]
rs4981770	1.00[YRI][hapmap]
rs58049	1.00[YRI][hapmap]
rs7144204	1.00[YRI][hapmap]
rs7147530	1.00[YRI][hapmap]
rs7153509	1.00[YRI][hapmap]
rs8006314	1.00[YRI][hapmap]
rs9806111	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv564169	chr14:30819087-31541494	Strong transcription Genic enhancers ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv1036419	chr14:30969616-31224226	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv901581	chr14:30978745-31585289	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
4	nsv564171	chr14:31068090-31149630	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12432098	SCFD1	cis	parietal	SCAN
rs12432098	SCFD1	cis	cerebellum	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:31043000-31090600	Weak transcription	Small Intestine	intestine
2	chr14:31053800-31090600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr14:31069000-31090600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr14:31069000-31090800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr14:31070400-31090600	Weak transcription	Spleen	Spleen
6	chr14:31071000-31090600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr14:31071000-31090600	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr14:31071400-31090800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr14:31072400-31090600	Weak transcription	Lung	lung
10	chr14:31073800-31090600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr14:31074400-31090600	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr14:31080000-31090600	Weak transcription	Fetal Brain Male	brain
13	chr14:31080400-31090600	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr14:31080400-31090600	Weak transcription	Esophagus	oesophagus
15	chr14:31080400-31090600	Weak transcription	Gastric	stomach
16	chr14:31080400-31090600	Weak transcription	HSMMtube	muscle
17	chr14:31080600-31090600	Weak transcription	Fetal Heart	heart
18	chr14:31084000-31090600	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr14:31085600-31090800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr14:31086000-31090600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr14:31086600-31090600	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr14:31086600-31090600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr14:31086800-31090800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr14:31087000-31090800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr14:31087200-31090600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr14:31087400-31090600	Weak transcription	HSMM	muscle
27	chr14:31087800-31090600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr14:31087800-31090600	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr14:31088000-31090600	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr14:31089600-31090800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr14:31089800-31090800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
32	chr14:31090200-31090600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr14:31090200-31090600	Active TSS	Skeletal Muscle Male	skeletal muscle
34	chr14:31090200-31090800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr14:31090200-31090800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
36	chr14:31090200-31090800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
37	chr14:31090200-31091200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
38	chr14:31090200-31091200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr14:31090200-31091200	Flanking Active TSS	GM12878-XiMat	blood
40	chr14:31090200-31091400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr14:31090200-31091400	Flanking Active TSS	Osteobl	bone
42	chr14:31090200-31092400	Active TSS	Duodenum Mucosa	Duodenum
43	chr14:31090200-31092400	Active TSS	Duodenum Smooth Muscle	Duodenum
44	chr14:31090200-31092400	Active TSS	Pancreatic Islets	Pancreatic Islet
45	chr14:31090200-31092400	Active TSS	Placenta	Placenta
46	chr14:31090200-31092400	Active TSS	Rectal Mucosa Donor 29	rectum
47	chr14:31090200-31092600	Active TSS	Rectal Mucosa Donor 31	rectum
48	chr14:31090200-31092800	Active TSS	Fetal Intestine Large	intestine
49	chr14:31090200-31092800	Active TSS	Psoas Muscle	Psoas
50	chr14:31090200-31093000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin

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