Variant report

Variant	rs4457912
Chromosome Location	chr14:56050896-56050897
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:20)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:20 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RCOR1	chr14:56050525-56050915	K562	blood:	n/a	n/a
2	RCOR1	chr14:56050605-56050983	K562	blood:	n/a	n/a
3	EP300	chr14:56050591-56050922	SK-N-SH_RA	brain:	n/a	n/a
4	CEBPB	chr14:56050893-56051269	HepG2	liver:	n/a	chr14:56051080-56051091
5	GATA3	chr14:56050454-56051092	SH-SY5Y	brain:	n/a	n/a
6	GATA2	chr14:56050433-56051230	SH-SY5Y	brain:	n/a	n/a
7	CEBPB	chr14:56050575-56051344	Hela-S3	cervix:	n/a	chr14:56051080-56051091
8	TCF7L2	chr14:56050538-56051238	HEK293	kidney:	n/a	n/a
9	GATA3	chr14:56050468-56051064	SK-N-SH	brain:	n/a	n/a
10	MAX	chr14:56050476-56051290	Hela-S3	cervix:	n/a	n/a
11	WRNIP1	chr14:56050479-56051019	GM12878	blood:	n/a	n/a
12	KAP1	chr14:56050493-56051465	U2OS	brain:	n/a	n/a
13	KAP1	chr14:56050300-56051476	HEK293	kidney:	n/a	n/a
14	CEBPB	chr14:56050895-56051272	IMR90	lung:	n/a	chr14:56051080-56051091
15	RCOR1	chr14:56050664-56051227	Hela-S3	cervix:	n/a	n/a
16	CCNT2	chr14:56050706-56051046	K562	blood:	n/a	n/a
17	FOXA1	chr14:56050836-56051363	HepG2	liver:	n/a	n/a
18	POLR2A	chr14:56050308-56051496	HepG2	liver:	n/a	n/a
19	ZNF263	chr14:56050375-56051394	HEK293-T-REx	kidney:	n/a	n/a
20	FOXA1	chr14:56050859-56051239	HepG2	liver:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr14:56050224..56053643-chr14:56057156..56060698,4	MCF-7	breast:
2	chr14:56047540..56051954-chr14:56053859..56059782,6	K562	blood:
3	chr14:56050702..56052550-chr14:56072121..56074340,2	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FBXO34-2	chr14:56050822-56050988	ucscGeneNc_uc001xci_2

No data

Variant related genes	Relation type
KTN1-AS1	TF binding region

Extended variants
information (count: 86 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10136386	0.88[CEU][hapmap]
rs10146870	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10444721	1.00[CEU][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10483644	0.81[JPT][hapmap]
rs10483649	1.00[ASW][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs10483651	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12432588	0.86[ASN][1000 genomes]
rs12432887	0.81[JPT][hapmap];0.82[MEX][hapmap]
rs12433592	0.86[ASN][1000 genomes]
rs12434609	0.84[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs12434799	0.85[ASN][1000 genomes]
rs12435643	0.81[JPT][hapmap]
rs12587735	1.00[CEU][hapmap];0.86[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.80[YRI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12589867	0.87[ASN][1000 genomes]
rs12590388	0.81[JPT][hapmap];0.82[MEX][hapmap]
rs12590936	0.81[JPT][hapmap]
rs12882850	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12891129	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12891526	0.85[AFR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12893162	0.93[ASW][hapmap];0.95[CEU][hapmap];0.93[GIH][hapmap];0.84[MEX][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12895070	0.86[ASN][1000 genomes]
rs12895366	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12897227	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17128610	0.93[ASN][1000 genomes]
rs17128614	0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs17128655	0.85[ASN][1000 genomes]
rs17128657	0.81[JPT][hapmap]
rs17128684	0.81[JPT][hapmap];0.82[MEX][hapmap]
rs17253737	0.83[EUR][1000 genomes]
rs17684916	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17684959	0.96[CEU][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17685650	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1951887	0.93[ASW][hapmap];1.00[CEU][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1951889	0.81[JPT][hapmap]
rs1951890	1.00[ASW][hapmap];0.84[CHD][hapmap];0.89[JPT][hapmap]
rs2093800	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2252189	0.81[JPT][hapmap]
rs2274076	0.81[JPT][hapmap]
rs2274078	0.81[JPT][hapmap]
rs2296182	0.93[ASW][hapmap];1.00[CEU][hapmap];0.85[JPT][hapmap]
rs2296183	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2341889	0.93[ASN][1000 genomes]
rs28581272	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34118806	0.87[ASN][1000 genomes]
rs34133022	0.83[EUR][1000 genomes]
rs34184813	0.85[ASN][1000 genomes]
rs34706911	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34853759	0.83[EUR][1000 genomes]
rs34931260	0.93[ASN][1000 genomes]
rs34982220	0.87[EUR][1000 genomes]
rs35047443	0.89[ASN][1000 genomes]
rs35420484	0.93[ASN][1000 genomes]
rs35451981	0.93[ASN][1000 genomes]
rs35531912	0.95[ASN][1000 genomes]
rs35560341	0.86[ASN][1000 genomes]
rs35790844	0.87[ASN][1000 genomes]
rs3765515	1.00[CEU][hapmap];0.81[JPT][hapmap];0.80[YRI][hapmap]
rs4901592	0.83[EUR][1000 genomes]
rs4901593	0.83[EUR][1000 genomes]
rs55760841	0.93[ASN][1000 genomes]
rs55927221	0.87[EUR][1000 genomes]
rs61381603	0.86[ASN][1000 genomes]
rs6573051	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6573053	0.96[CEU][hapmap];0.81[JPT][hapmap];0.80[YRI][hapmap];0.82[EUR][1000 genomes]
rs6573054	1.00[CEU][hapmap];0.81[JPT][hapmap];0.96[YRI][hapmap];0.84[EUR][1000 genomes]
rs68127620	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7150285	0.93[ASW][hapmap];0.87[CEU][hapmap];0.93[GIH][hapmap];0.89[LWK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7154548	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7156566	0.81[JPT][hapmap]
rs7158176	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs72719463	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8006443	0.86[ASN][1000 genomes]
rs8007183	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8007832	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8008764	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8011252	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8011732	0.80[CEU][hapmap]
rs942317	0.81[CEU][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	nsv901960	chr14:55853724-56085130	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	nsv901961	chr14:55853724-56101879	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	nsv901962	chr14:55862956-56101879	Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
4	nsv901963	chr14:55871452-56085130	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	nsv901964	chr14:55871452-56101879	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
6	nsv1051564	chr14:55895610-56130788	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
7	nsv542103	chr14:55895610-56130788	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
8	nsv901965	chr14:55976428-56101879	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs4457912	GCH1	cis	cerebellum	SCAN
rs4457912	FBXO34	cis	parietal	SCAN
rs4457912	CNIH	cis	cerebellum	SCAN
rs4457912	KTN1	cis	multi-tissue	Pritchard
rs4457912	GCH1	cis	parietal	SCAN
rs4457912	KTN1	cis	cerebellum	SCAN
rs4457912	KTN1	cis	parietal	SCAN

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:56045600-56051000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr14:56048200-56054200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
3	chr14:56048200-56068400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr14:56048400-56052000	Enhancers	Primary B cells from peripheral blood	blood
5	chr14:56048400-56052800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr14:56048400-56055200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
7	chr14:56048400-56056000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr14:56048400-56068400	Weak transcription	Esophagus	oesophagus
9	chr14:56048400-56086000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr14:56048600-56051200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr14:56048600-56051200	Enhancers	Duodenum Smooth Muscle	Duodenum
12	chr14:56048600-56051400	Enhancers	Primary hematopoietic stem cells	blood
13	chr14:56048600-56051400	Enhancers	Rectal Smooth Muscle	rectum
14	chr14:56048600-56051600	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr14:56048600-56051600	Enhancers	Primary T killer memory cells from peripheral blood	blood
16	chr14:56048600-56052400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr14:56048600-56052400	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr14:56048600-56052800	Weak transcription	Thymus	Thymus
19	chr14:56048600-56053000	Enhancers	Primary T helper naive cells from peripheral blood	blood
20	chr14:56048600-56053600	Enhancers	Osteobl	bone
21	chr14:56048600-56054000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
22	chr14:56048600-56055400	Enhancers	Primary T helper cells fromperipheralblood	blood
23	chr14:56048600-56055400	Enhancers	Liver	Liver
24	chr14:56048600-56058400	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr14:56048600-56060400	Weak transcription	Brain Substantia Nigra	brain
26	chr14:56048600-56070800	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr14:56048800-56051000	Enhancers	NHDF-Ad	bronchial
28	chr14:56048800-56051200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr14:56048800-56051400	Enhancers	Pancreatic Islets	Pancreatic Islet
30	chr14:56048800-56055000	Enhancers	Muscle Satellite Cultured Cells	--
31	chr14:56049000-56051200	Enhancers	HUES48 Cell Line	embryonic stem cell
32	chr14:56049000-56051200	Enhancers	Primary hematopoietic stem cells short term culture	blood
33	chr14:56049000-56051200	Enhancers	Dnd41	blood
34	chr14:56049000-56051800	Enhancers	HepG2	liver
35	chr14:56049000-56052400	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr14:56049200-56051600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
37	chr14:56049200-56051600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr14:56049200-56051600	Enhancers	Colon Smooth Muscle	Colon
39	chr14:56049200-56055200	Enhancers	Primary T cells from cord blood	blood
40	chr14:56049400-56051200	Enhancers	NHLF	lung
41	chr14:56049400-56051400	Enhancers	Primary monocytes fromperipheralblood	blood
42	chr14:56049400-56051600	Enhancers	HSMM	muscle
43	chr14:56049600-56051000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
44	chr14:56049600-56051200	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr14:56049600-56051600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr14:56049600-56051800	Enhancers	Stomach Mucosa	stomach
47	chr14:56049600-56052000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr14:56049600-56052000	Weak transcription	HUVEC	blood vessel
49	chr14:56049600-56052400	Enhancers	HSMMtube	muscle
50	chr14:56049600-56053000	Enhancers	Fetal Intestine Small	intestine

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