Variant report

Variant	rs10146759
Chromosome Location	chr14:24899194-24899195
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:330)
CpG islands
(count:0)
Chromatin interactive
region (count:36)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:330 , 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	TAF1	chr14:24898794-24899604	HepG2	liver:	n/a	n/a
2	MYC	chr14:24898910-24899686	K562	blood:	n/a	n/a
3	JUND	chr14:24898906-24899549	HepG2	liver:	n/a	chr14:24899146-24899154
4	CREB1	chr14:24898883-24899729	A549	lung:	n/a	n/a
5	POLR2A	chr14:24898243-24900199	ECC-1	luminal epithelium:	n/a	n/a
6	GTF2F1	chr14:24898925-24899196	H1-hESC	embryonic stem cell:	n/a	n/a
7	TBL1XR1	chr14:24898931-24899275	K562	blood:	n/a	n/a
8	POLR2A	chr14:24898745-24899627	PANC-1	pancreas:	n/a	n/a
9	CHD2	chr14:24899019-24899532	H1-hESC	embryonic stem cell:	n/a	n/a
10	SPI1	chr14:24898918-24899262	GM12878	blood:	n/a	n/a
11	KAT2A	chr14:24899116-24899283	GM12878	blood:	n/a	n/a
12	CREB1	chr14:24898988-24899293	A549	lung:	n/a	n/a
13	MAZ	chr14:24898592-24900245	K562	blood:	n/a	chr14:24898793-24898803
14	HEY1	chr14:24898468-24900380	HepG2	liver:	n/a	n/a
15	JUND	chr14:24898871-24900049	K562	blood:	n/a	chr14:24899146-24899154
16	POLR2A	chr14:24898659-24900027	U87	brain:	n/a	n/a
17	POLR2A	chr14:24898480-24900532	GM12891	blood:	n/a	n/a
18	PML	chr14:24898852-24899275	GM12878	blood:	n/a	n/a
19	POLR2A	chr14:24898739-24899896	Hela-S3	cervix:	n/a	n/a
20	HEY1	chr14:24898829-24899826	HepG2	liver:	n/a	n/a
21	SIN3AK20	chr14:24898740-24899942	HepG2	liver:	n/a	n/a
22	HNF4A	chr14:24898917-24899658	HepG2	liver:	n/a	chr14:24899515-24899528 chr14:24899515-24899528
23	POLR2A	chr14:24898863-24899377	K562	blood:	n/a	n/a
24	E2F4	chr14:24898929-24899297	MCF10A-Er-Src	breast:	n/a	chr14:24899079-24899088 chr14:24899256-24899265 chr14:24899077-24899087
25	STAT3	chr14:24898843-24899245	MCF10A-Er-Src	breast:	n/a	n/a
26	SIN3A	chr14:24898327-24900163	H1-hESC	embryonic stem cell:	n/a	chr14:24899282-24899291 chr14:24899100-24899111
27	TAF1	chr14:24898855-24899753	K562	blood:	n/a	n/a
28	POLR2A	chr14:24898379-24899365	GM12892	blood:	n/a	n/a
29	MAZ	chr14:24898402-24901483	IMR90	lung:	n/a	chr14:24898793-24898803
30	GABPA	chr14:24898967-24899340	SK-N-SH	brain:	n/a	chr14:24899256-24899265
31	POLR2A	chr14:24898571-24900371	GM12878	blood:	n/a	n/a
32	POLR2A	chr14:24898440-24900415	GM19193	blood:	n/a	n/a
33	POLR2A	chr14:24898647-24900232	MCF10A-Er-Src	breast:	n/a	n/a
34	RFX5	chr14:24898870-24899651	Hela-S3	cervix:	n/a	n/a
35	FOXP2	chr14:24898932-24899221	PFSK-1	brain:	n/a	n/a
36	BCLAF1	chr14:24898770-24899536	GM12878	blood:	n/a	chr14:24899077-24899086 chr14:24899209-24899218 chr14:24899074-24899083 chr14:24899252-24899265 chr14:24899099-24899112 chr14:24899075-24899088
37	FOS	chr14:24899067-24899210	MCF10A-Er-Src	breast:	n/a	chr14:24899146-24899154
38	RCOR1	chr14:24898888-24899681	HepG2	liver:	n/a	n/a
39	TAF7	chr14:24898944-24899601	H1-hESC	embryonic stem cell:	n/a	n/a
40	MAFK	chr14:24899169-24899204	H1-hESC	embryonic stem cell:	n/a	n/a
41	POLR2A	chr14:24898737-24899637	PANC-1	pancreas:	n/a	n/a
42	POLR2A	chr14:24898824-24899751	K562	blood:	n/a	n/a
43	MAX	chr14:24898744-24899447	ECC-1	luminal epithelium:	n/a	chr14:24898793-24898803
44	POU2F2	chr14:24898778-24899291	GM12878	blood:	n/a	n/a
45	CEBPD	chr14:24898797-24899412	K562	blood:	n/a	n/a
46	RFX5	chr14:24898888-24899298	HepG2	liver:	n/a	n/a
47	TAL1	chr14:24898964-24899312	K562	blood:	n/a	n/a
48	POLR2A	chr14:24898788-24900109	HCT-116	colon:	n/a	n/a
49	UBTF	chr14:24898784-24900227	K562	blood:	n/a	n/a
50	RELA	chr14:24898678-24901293	GM10847	blood:	n/a	chr14:24900296-24900305 chr14:24900296-24900305

No data

(count:36 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr14:24681602..24685045-chr14:24898549..24902277,4	MCF-7	breast:
2	chr1:17222179..17223065-chr14:24899159..24900024,3	Hela-S3	cervix:
3	chr14:24833553..24839988-chr14:24894553..24902357,9	K562	blood:
4	chr14:24899081..24899637-chr3:19988552..19989514,2	Hela-S3	cervix:
5	chr14:24663295..24665382-chr14:24899130..24900830,2	MCF-7	breast:
6	chr14:24710331..24713124-chr14:24894765..24900704,5	MCF-7	breast:
7	chr14:24898746..24899612-chr14:24911431..24912345,3	Hela-S3	cervix:
8	chr1:150550930..150551451-chr14:24899156..24899739,2	Hela-S3	cervix:
9	chr14:24833707..24839988-chr14:24896546..24902736,10	K562	blood:
10	chr14:24816528..24849574-chr14:24893305..24914155,145	MCF-7	breast:
11	chr14:24898542..24899536-chr19:39421414..39422162,2	HCT-116	colon:
12	chr14:24789439..24822082-chr14:24898039..24913135,99	MCF-7	breast:
13	chr11:60927487..60929206-chr14:24898894..24900435,2	MCF-7	breast:
14	chr14:24898627..24899513-chr15:65588184..65589308,3	Hela-S3	cervix:
15	chr14:24857849..24868599-chr14:24892485..24903992,27	MCF-7	breast:
16	chr14:24899048..24899703-chr3:49130413..49131180,2	NB4	blood:
17	chr14:24791358..24808812-chr14:24895309..24913599,55	K562	blood:
18	chr14:24700875..24703033-chr14:24898892..24902478,3	MCF-7	breast:
19	chr14:24709552..24713134-chr14:24898718..24901467,5	MCF-7	breast:
20	chr14:24801289..24801981-chr14:24899000..24899921,2	K562	blood:
21	chr14:24827418..24850855-chr14:24894884..24913772,127	MCF-7	breast:
22	chr14:24700052..24703046-chr14:24899147..24901202,2	K562	blood:
23	chr14:24781460..24810019-chr14:24892340..24914262,110	MCF-7	breast:
24	chr14:24705394..24707456-chr14:24899113..24901085,2	MCF-7	breast:
25	chr14:24845008..24848281-chr14:24897427..24900354,3	K562	blood:
26	chr14:24766804..24771569-chr14:24898237..24903800,5	MCF-7	breast:
27	chr14:24779448..24783163-chr14:24897934..24900807,3	MCF-7	breast:
28	chr14:24800528..24803981-chr14:24898784..24901810,5	K562	blood:
29	chr14:24898646..24899247-chr5:162864084..162865047,2	Hela-S3	cervix:
30	chr14:24863920..24868653-chr14:24896299..24901214,6	MCF-7	breast:
31	chr14:24609424..24612056-chr14:24897977..24900717,2	MCF-7	breast:
32	chr14:24765284..24770509-chr14:24899183..24903551,4	MCF-7	breast:
33	chr14:24711225..24713495-chr14:24896859..24899429,2	K562	blood:
34	chr14:24796459..24799989-chr14:24897944..24901736,5	K562	blood:
35	chr14:24768412..24770961-chr14:24898867..24900397,2	K562	blood:
36	chr14:24732224..24734539-chr14:24898247..24900627,2	MCF-7	breast:

No data

Variant related genes	Relation type
CBLN3	TF binding region
KHNYN	TF binding region
ENSG00000205978	Chromatin interaction
ENSG00000104835	Chromatin interaction
ENSG00000129559	Chromatin interaction
ENSG00000213903	Chromatin interaction
ENSG00000136305	Chromatin interaction
ENSG00000128626	Chromatin interaction
ENSG00000129465	Chromatin interaction
ENSG00000255526	Chromatin interaction
ENSG00000143384	Chromatin interaction
ENSG00000196943	Chromatin interaction
ENSG00000167987	Chromatin interaction
ENSG00000100938	Chromatin interaction
ENSG00000199568	Chromatin interaction
ENSG00000100926	Chromatin interaction
ENSG00000254692	Chromatin interaction
ENSG00000129467	Chromatin interaction
ENSG00000250061	Chromatin interaction
ENSG00000092330	Chromatin interaction
ENSG00000144566	Chromatin interaction
ENSG00000100968	Chromatin interaction
ENSG00000113328	Chromatin interaction
ENSG00000258973	Chromatin interaction
ENSG00000207005	Chromatin interaction
ENSG00000213920	Chromatin interaction
ENSG00000157379	Chromatin interaction
ENSG00000254505	Chromatin interaction
ENSG00000100908	Chromatin interaction
ENSG00000092295	Chromatin interaction
ENSG00000198218	Chromatin interaction
ENSG00000100445	Chromatin interaction
ENSG00000207141	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11158709	1.00[CHB][hapmap]
rs11622667	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12891613	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1473723	1.00[CHB][hapmap]
rs1473724	1.00[CHB][hapmap]
rs1473726	1.00[CHB][hapmap]
rs1956891	1.00[CHB][hapmap]
rs1956892	1.00[CHB][hapmap]
rs1956894	1.00[CHB][hapmap]
rs1956895	1.00[CHB][hapmap]
rs1956897	1.00[CHB][hapmap]
rs2332332	1.00[CHB][hapmap]
rs4390517	1.00[CHB][hapmap]
rs4981515	1.00[CHB][hapmap]
rs4982915	1.00[CHB][hapmap]
rs4982922	1.00[CHB][hapmap]
rs4982923	1.00[CHB][hapmap]
rs4982924	1.00[CHB][hapmap]
rs4982925	1.00[CHB][hapmap]
rs4982926	1.00[CHB][hapmap]
rs7143047	1.00[CHB][hapmap]
rs7149255	1.00[CHB][hapmap]
rs7151995	1.00[CHD][hapmap];0.81[ASN][1000 genomes]
rs8005307	0.93[ASN][1000 genomes]
rs8013354	1.00[CHB][hapmap]
rs911369	1.00[CHB][hapmap]
rs911370	1.00[CHB][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	nsv1041336	chr14:24726564-25527319	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
2	nsv542000	chr14:24726564-25527319	Genic enhancers Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	107 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs10146759	CBLN3,KHNYN	cis	brain	BrainEAC
rs10146759	KIAA0323	Cis_1M	lymphoblastoid	RTeQTL
rs10146759	KHNYN	cis	Whole Blood	GTEx
rs10146759	KHNYN	cis	cerebellum	SCAN
rs10146759	CBLN3	cis	parietal	SCAN
rs10146759	CBLN3	Cis_1M	lymphoblastoid	RTeQTL
rs10146759	OR4Q3	cis	cerebellum	SCAN
rs10146759	THTPA	cis	cerebellum	SCAN
rs10146759	KHNYN	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:24898000-24899600	Enhancers	Fetal Heart	heart
2	chr14:24898200-24899200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr14:24898200-24899200	Flanking Active TSS	Stomach Smooth Muscle	stomach
4	chr14:24898400-24899200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr14:24898400-24899200	Enhancers	HUVEC	blood vessel
6	chr14:24898400-24899600	Enhancers	Fetal Brain Male	brain
7	chr14:24898400-24900000	Active TSS	HSMM	muscle
8	chr14:24898600-24899200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr14:24898600-24899800	Active TSS	Brain Angular Gyrus	brain
10	chr14:24898600-24900000	Active TSS	Duodenum Smooth Muscle	Duodenum
11	chr14:24898600-24900200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
12	chr14:24898600-24900200	Active TSS	Fetal Kidney	kidney
13	chr14:24898600-24900600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
14	chr14:24898600-24900600	Active TSS	Ovary	ovary
15	chr14:24898600-24900800	Active TSS	HSMMtube	muscle
16	chr14:24898600-24901000	Active TSS	H9 Cell Line	embryonic stem cell
17	chr14:24898800-24899200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr14:24898800-24899200	Flanking Active TSS	HMEC	breast
19	chr14:24898800-24899600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
20	chr14:24898800-24899600	Active TSS	Primary T cells from cord blood	blood
21	chr14:24898800-24899600	Active TSS	Brain Inferior Temporal Lobe	brain
22	chr14:24898800-24899600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
23	chr14:24898800-24899600	Active TSS	Skeletal Muscle Female	skeletal muscle
24	chr14:24898800-24899800	Active TSS	Brain Anterior Caudate	brain
25	chr14:24898800-24900000	Active TSS	HUES6 Cell Line	embryonic stem cell
26	chr14:24898800-24900000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr14:24898800-24900000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr14:24898800-24900000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr14:24898800-24900000	Active TSS	Left Ventricle	heart
30	chr14:24898800-24900000	Active TSS	Spleen	Spleen
31	chr14:24898800-24900200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr14:24898800-24900200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr14:24898800-24900200	Active TSS	iPS-15b Cell Line	embryonic stem cell
34	chr14:24898800-24900200	Active TSS	Colon Smooth Muscle	Colon
35	chr14:24898800-24900200	Active TSS	Small Intestine	intestine
36	chr14:24898800-24900400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr14:24898800-24900400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
38	chr14:24898800-24900400	Active TSS	Aorta	Aorta
39	chr14:24898800-24900400	Active TSS	Psoas Muscle	Psoas
40	chr14:24898800-24900400	Active TSS	NHLF	lung
41	chr14:24898800-24900600	Flanking Active TSS	Primary hematopoietic stem cells	blood
42	chr14:24898800-24900600	Active TSS	Pancreatic Islets	Pancreatic Islet
43	chr14:24898800-24900800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr14:24898800-24900800	Active TSS	Right Atrium	heart
45	chr14:24899000-24899200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
46	chr14:24899000-24899200	Weak transcription	Gastric	stomach
47	chr14:24899000-24899400	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
48	chr14:24899000-24899400	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr14:24899000-24899600	Active TSS	H1 Cell Line	embryonic stem cell
50	chr14:24899000-24899600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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