Variant report

Variant	rs1057536
Chromosome Location	chr14:38063120-38063121
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MBD4	chr14:38062469-38066000	HepG2	liver:	n/a	n/a
2	ARID3A	chr14:38062570-38065874	HepG2	liver:	n/a	n/a
3	POLR2A	chr14:38063093-38065769	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr14:38062953-38066652	MCF10A-Er-Src	breast:	n/a	n/a
5	JUND	chr14:38062628-38066066	MCF-7	breast:	n/a	chr14:38064795-38064804 chr14:38065116-38065126 chr14:38063103-38063111 chr14:38065214-38065223 chr14:38063106-38063118 chr14:38064080-38064089 chr14:38065116-38065126 chr14:38062672-38062682 chr14:38065212-38065223 chr14:38065116-38065126 chr14:38064791-38064800 chr14:38063103-38063110 chr14:38065396-38065405 chr14:38065116-38065126 chr14:38063967-38063976 chr14:38065213-38065222
6	SIN3AK20	chr14:38060259-38066080	MCF-7	breast:	n/a	n/a
7	STAT3	chr14:38063069-38063134	MCF10A-Er-Src	breast:	n/a	n/a
8	CTCF	chr14:38062980-38063865	K562	blood:	n/a	chr14:38063551-38063569 chr14:38063553-38063566 chr14:38063546-38063567 chr14:38063552-38063568
9	ZNF263	chr14:38062768-38066049	HEK293-T-REx	kidney:	n/a	chr14:38065390-38065399 chr14:38064974-38064983
10	POLR2A	chr14:38061993-38063784	H1-neurons	neurons:	n/a	n/a
11	EP300	chr14:38062686-38065992	MCF-7	breast:	n/a	chr14:38063806-38063822 chr14:38063793-38063809 chr14:38064922-38064938 chr14:38065416-38065429
12	GATA3	chr14:38062684-38064001	MCF-7	breast:	n/a	chr14:38063101-38063110 chr14:38062965-38062981
13	BRCA1	chr14:38063097-38063799	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr14:38059290-38065931	MCF-7	breast:	n/a	n/a
15	MYBL2	chr14:38062961-38065996	HepG2	liver:	n/a	n/a
16	JUND	chr14:38062687-38063847	T-47D	breast:	n/a	chr14:38063103-38063111 chr14:38063106-38063118 chr14:38063103-38063110
17	NFIC	chr14:38063076-38064013	HepG2	liver:	n/a	n/a
18	TEAD4	chr14:38062782-38063848	HepG2	liver:	n/a	n/a
19	CTCF	chr14:38063042-38064519	A549	lung:	n/a	chr14:38063551-38063569 chr14:38063553-38063566 chr14:38063546-38063567 chr14:38063552-38063568
20	FOS	chr14:38062960-38063617	MCF10A-Er-Src	breast:	n/a	chr14:38063103-38063111 chr14:38063106-38063118 chr14:38063103-38063110
21	POLR2A	chr14:38062485-38064337	HepG2	liver:	n/a	n/a
22	TCF12	chr14:38063010-38065993	MCF-7	breast:	n/a	chr14:38063914-38063924 chr14:38063377-38063384 chr14:38065551-38065559
23	POLR2A	chr14:38063064-38065581	MCF10A-Er-Src	breast:	n/a	n/a
24	HDAC2	chr14:38063100-38067230	MCF-7	breast:	n/a	chr14:38066217-38066231 chr14:38064284-38064293 chr14:38066216-38066230 chr14:38063289-38063303 chr14:38063290-38063304 chr14:38066214-38066228 chr14:38066207-38066221 chr14:38066181-38066195 chr14:38064764-38064778 chr14:38065036-38065050 chr14:38066212-38066226 chr14:38066211-38066225 chr14:38066176-38066190 chr14:38066215-38066229 chr14:38065033-38065047 chr14:38066213-38066227 chr14:38065035-38065049 chr14:38064765-38064779 chr14:38066210-38066224
25	POLR2A	chr14:38061996-38063915	H1-neurons	neurons:	n/a	n/a
26	RAD21	chr14:38063046-38064364	HepG2	liver:	n/a	chr14:38063549-38063568
27	HEY1	chr14:38061267-38065955	HepG2	liver:	n/a	chr14:38065572-38065587 chr14:38064280-38064295 chr14:38063965-38063980 chr14:38064069-38064084 chr14:38064057-38064072 chr14:38063797-38063812
28	ZNF217	chr14:38062815-38063887	MCF-7	breast:	n/a	n/a
29	RAD21	chr14:38063020-38063806	HepG2	liver:	n/a	chr14:38063549-38063568
30	PML	chr14:38062592-38065777	MCF-7	breast:	n/a	n/a
31	MYBL2	chr14:38062913-38066214	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:120729261..120730769-chr14:38062187..38064055,2	MCF-7	breast:
2	chr14:38055708..38063394-chr14:38063498..38068319,8	K562	blood:
3	chr14:38061626..38064274-chr8:144362134..144365132,2	MCF-7	breast:
4	chr14:37731472..37733246-chr14:38060600..38063260,2	MCF-7	breast:
5	chr14:37664939..37667912-chr14:38062947..38065316,3	MCF-7	breast:
6	chr14:38062598..38064269-chr16:87798800..87800930,2	MCF-7	breast:
7	chr14:38061973..38064113-chr8:48650908..48653008,2	MCF-7	breast:
8	chr14:37709149..37730989-chr14:38048141..38067789,135	MCF-7	breast:
9	chr14:21736096..21738321-chr14:38062641..38065635,3	MCF-7	breast:
10	chr12:133136306..133139084-chr14:38062974..38065575,2	MCF-7	breast:
11	chr14:38035549..38036658-chr14:38063068..38063787,3	MCF-7	breast:
12	chr14:37708906..37733371-chr14:38048131..38068843,170	MCF-7	breast:
13	chr14:38061358..38063507-chr3:161089489..161091930,2	MCF-7	breast:
14	chr14:37903287..37907312-chr14:38059908..38064571,5	MCF-7	breast:
15	chr14:38062286..38064819-chr20:46129105..46132077,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SLC25A21-3	chr14:38063080-38063818	NONHSAT036465

Variant related genes	Relation type
TTC6	TF binding region
ENSG00000112787	Chromatin interaction
ENSG00000253716	Chromatin interaction
ENSG00000129514	Chromatin interaction
ENSG00000259087	Chromatin interaction
ENSG00000104731	Chromatin interaction
ENSG00000207046	Chromatin interaction
ENSG00000092199	Chromatin interaction
ENSG00000124151	Chromatin interaction
ENSG00000151338	Chromatin interaction
ENSG00000139865	Chromatin interaction
ENSG00000196542	Chromatin interaction
ENSG00000221869	Chromatin interaction
ENSG00000202538	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs1008236	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.92[JPT][hapmap];0.87[LWK][hapmap];0.90[MEX][hapmap];0.92[TSI][hapmap];0.83[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10133438	0.82[CEU][hapmap];0.86[CHB][hapmap]
rs10143976	0.91[CHD][hapmap];0.93[GIH][hapmap];0.84[TSI][hapmap]
rs10144334	0.85[ASN][1000 genomes]
rs10145379	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10145473	0.86[CHB][hapmap];0.91[CHD][hapmap];0.85[ASN][1000 genomes]
rs10149161	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10151200	0.86[CHB][hapmap]
rs10400689	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap]
rs11156961	0.86[CHB][hapmap];0.91[CHD][hapmap];0.85[ASN][1000 genomes]
rs11156962	0.82[CEU][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];0.98[GIH][hapmap];0.89[TSI][hapmap];0.85[ASN][1000 genomes]
rs1155456	0.91[CHD][hapmap];0.93[GIH][hapmap];0.84[TSI][hapmap]
rs1158701	0.86[CHB][hapmap]
rs1159151	0.82[CEU][hapmap];0.86[CHB][hapmap]
rs11623989	0.87[CHD][hapmap];0.95[GIH][hapmap]
rs11627807	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11627844	0.82[CEU][hapmap];0.81[CHD][hapmap];0.92[JPT][hapmap];0.85[MEX][hapmap];0.87[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1169873	0.91[CHD][hapmap];0.95[GIH][hapmap];0.84[TSI][hapmap]
rs11846416	0.85[ASN][1000 genomes]
rs12894536	0.83[CHD][hapmap];0.84[TSI][hapmap]
rs12896760	0.83[CHD][hapmap];0.84[TSI][hapmap]
rs1547009	0.82[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];0.89[TSI][hapmap]
rs17179078	0.83[CHD][hapmap];0.84[TSI][hapmap]
rs17768249	0.83[CHD][hapmap];0.81[TSI][hapmap]
rs1814005	0.91[CHD][hapmap];0.93[GIH][hapmap];0.84[TSI][hapmap]
rs1884798	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1884803	0.86[CHB][hapmap];0.91[CHD][hapmap]
rs1950824	0.86[CHB][hapmap];0.91[CHD][hapmap]
rs1950826	0.86[CHB][hapmap];0.91[CHD][hapmap];0.85[ASN][1000 genomes]
rs1955934	0.87[CHD][hapmap];0.86[TSI][hapmap]
rs1955943	0.83[CHD][hapmap]
rs1955949	0.84[TSI][hapmap]
rs1956427	0.91[CHD][hapmap];0.93[GIH][hapmap];0.84[TSI][hapmap]
rs1956429	0.97[ASN][1000 genomes]
rs1956433	0.91[CHD][hapmap];0.95[GIH][hapmap];0.84[TSI][hapmap]
rs1956437	0.91[CHD][hapmap];0.95[GIH][hapmap]
rs1956442	0.85[CEU][hapmap];0.86[CHB][hapmap];0.85[ASN][1000 genomes]
rs1956443	0.81[CEU][hapmap];0.86[CHB][hapmap];0.85[ASN][1000 genomes]
rs1980675	0.86[CHB][hapmap];0.85[ASN][1000 genomes]
rs2006729	0.85[CHB][hapmap];0.87[CHD][hapmap];0.84[TSI][hapmap]
rs2146133	0.91[CHD][hapmap];0.93[GIH][hapmap];0.84[TSI][hapmap]
rs2180609	0.91[CHD][hapmap];0.95[GIH][hapmap];0.86[TSI][hapmap]
rs2415404	0.91[CHD][hapmap];0.95[GIH][hapmap]
rs4900918	0.91[CHD][hapmap];0.95[GIH][hapmap];0.83[TSI][hapmap]
rs4900945	0.91[CHD][hapmap];0.93[GIH][hapmap];0.86[TSI][hapmap]
rs4900969	0.86[CHB][hapmap];0.91[CHD][hapmap]
rs4901012	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6571812	0.83[CHD][hapmap];0.84[TSI][hapmap]
rs6571814	0.91[CHD][hapmap];0.93[GIH][hapmap];0.84[TSI][hapmap]
rs7144658	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7145671	0.81[CEU][hapmap];0.83[CHD][hapmap];0.84[TSI][hapmap]
rs7146299	0.91[CHD][hapmap];0.93[GIH][hapmap];0.84[TSI][hapmap]
rs7146958	0.85[ASN][1000 genomes]
rs7147379	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.92[JPT][hapmap];0.90[MEX][hapmap];0.92[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7153426	0.91[CHD][hapmap];0.95[GIH][hapmap];0.84[TSI][hapmap]
rs7153867	0.85[ASN][1000 genomes]
rs7159456	0.86[CHB][hapmap];0.91[CHD][hapmap];0.85[ASN][1000 genomes]
rs7160774	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7161228	0.92[ASN][1000 genomes]
rs7161326	0.90[CHD][hapmap];0.95[GIH][hapmap]
rs7493775	0.86[CHB][hapmap];0.91[CHD][hapmap];0.85[ASN][1000 genomes]
rs762083	0.97[ASN][1000 genomes]
rs8005136	0.87[CHD][hapmap]
rs8008655	0.83[CHD][hapmap]
rs8016138	0.85[ASN][1000 genomes]
rs8019713	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];0.92[JPT][hapmap];0.92[TSI][hapmap];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9322981	0.83[ASN][1000 genomes]
rs968350	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];0.92[JPT][hapmap];0.84[TSI][hapmap];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs996916	0.82[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];0.89[TSI][hapmap];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530038	chr14:37590543-38336191	Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv826923	chr14:38017619-38108645	Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
3	nsv832772	chr14:38030300-38225921	Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
4	nsv901642	chr14:38041870-38081005	Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
5	nsv901643	chr14:38047789-38081005	Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
6	nsv901644	chr14:38049107-38064738	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
7	nsv901645	chr14:38051035-38064215	Bivalent Enhancer Bivalent/Poised TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
8	nsv901646	chr14:38051035-38081005	Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Weak transcription Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
9	nsv901647	chr14:38052110-38064738	Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
10	nsv901648	chr14:38052110-38065813	Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
11	nsv916985	chr14:38052347-38838551	Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	59 gene(s)	inside rSNPs	diseases
12	nsv901649	chr14:38053334-38065813	Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
13	esv3405207	chr14:38062726-38066074	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Active TSS Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1057536	SEC23A	cis	parietal	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:38056200-38065600	Bivalent/Poised TSS	Fetal Intestine Small	intestine
2	chr14:38056400-38066000	Bivalent/Poised TSS	Fetal Intestine Large	intestine
3	chr14:38057000-38065400	Active TSS	Liver	Liver
4	chr14:38059600-38063200	Bivalent/Poised TSS	Stomach Mucosa	stomach
5	chr14:38059800-38065600	Active TSS	A549	lung
6	chr14:38060000-38063200	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
7	chr14:38060400-38064000	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
8	chr14:38060600-38064000	Bivalent/Poised TSS	Sigmoid Colon	Sigmoid Colon
9	chr14:38061400-38063200	Bivalent/Poised TSS	Fetal Stomach	stomach
10	chr14:38061800-38064600	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
11	chr14:38062200-38063400	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr14:38062200-38063400	Bivalent/Poised TSS	Fetal Lung	lung
13	chr14:38062200-38063600	Weak transcription	Pancreas	Pancrea
14	chr14:38062400-38063400	Weak transcription	Gastric	stomach
15	chr14:38062400-38063600	Weak transcription	Lung	lung
16	chr14:38062400-38064000	Active TSS	Colonic Mucosa	Colon
17	chr14:38062400-38064400	Active TSS	Small Intestine	intestine
18	chr14:38062400-38065200	Active TSS	Rectal Mucosa Donor 31	rectum
19	chr14:38062800-38063200	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr14:38062800-38063200	Flanking Active TSS	Hela-S3	cervix
21	chr14:38062800-38063400	Bivalent Enhancer	NHEK	skin
22	chr14:38062800-38063600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr14:38062800-38063600	Bivalent/Poised TSS	Esophagus	oesophagus
24	chr14:38062800-38065600	Bivalent/Poised TSS	HepG2	liver
25	chr14:38062800-38065600	Active TSS	K562	blood
26	chr14:38063000-38063400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr14:38063000-38065600	Active TSS	Rectal Mucosa Donor 29	rectum

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