Variant report

Variant	rs56089943
Chromosome Location	chr4:48342682-48342683
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	JUN	chr4:48342560-48343706	K562	blood:	n/a	chr4:48342747-48342758 chr4:48342726-48342735 chr4:48343389-48343398 chr4:48343239-48343248
2	POLR2A	chr4:48342228-48344387	H1-hESC	embryonic stem cell:	n/a	n/a
3	PML	chr4:48342508-48344642	GM12878	blood:	n/a	n/a
4	POLR2A	chr4:48342462-48343728	K562	blood:	n/a	n/a
5	UBTF	chr4:48342320-48345277	K562	blood:	n/a	n/a
6	KAP1	chr4:48342302-48343261	U2OS	brain:	n/a	n/a
7	POLR2A	chr4:48342555-48344209	MCF10A-Er-Src	breast:	n/a	n/a
8	NR2F2	chr4:48342426-48343797	K562	blood:	n/a	n/a
9	POLR2A	chr4:48342315-48344444	IMR90	lung:	n/a	n/a
10	FOXA1	chr4:48342603-48342866	T-47D	breast:	n/a	n/a
11	SIN3A	chr4:48342275-48344914	H1-hESC	embryonic stem cell:	n/a	chr4:48344167-48344178 chr4:48343390-48343401 chr4:48343422-48343431 chr4:48344167-48344180 chr4:48343093-48343104
12	POLR2A	chr4:48342498-48344353	PFSK-1	brain:	n/a	n/a
13	RUNX3	chr4:48342646-48343804	GM12878	blood:	n/a	n/a
14	POLR2A	chr4:48342366-48344589	K562	blood:	n/a	n/a
15	FOXA1	chr4:48342651-48343280	HepG2	liver:	n/a	n/a
16	TBP	chr4:48342551-48343291	Hela-S3	cervix:	n/a	n/a
17	EGR1	chr4:48342635-48342889	K562	blood:	n/a	n/a
18	POLR2A	chr4:48342593-48343788	HUVEC	blood vessel:	n/a	n/a
19	PML	chr4:48342370-48344072	K562	blood:	n/a	n/a
20	CTCF	chr4:48342660-48342753	K562	blood:	n/a	n/a
21	CHD1	chr4:48342148-48345930	IMR90	lung:	n/a	n/a
22	POLR2A	chr4:48342681-48344532	HL-60	blood:	n/a	n/a
23	MYC	chr4:48342295-48343743	NB4	blood:	n/a	n/a
24	RAD21	chr4:48342492-48344680	IMR90	lung:	n/a	chr4:48343576-48343589 chr4:48343424-48343438 chr4:48343397-48343411
25	ARID3A	chr4:48342653-48343056	K562	blood:	n/a	n/a
26	MXI1	chr4:48342390-48345427	SK-N-SH	brain:	n/a	n/a
27	UBTF	chr4:48342477-48344421	K562	blood:	n/a	n/a
28	EGR1	chr4:48342628-48342918	K562	blood:	n/a	n/a
29	TAF1	chr4:48342670-48342882	K562	blood:	n/a	n/a
30	MAZ	chr4:48342367-48344790	IMR90	lung:	n/a	n/a
31	TEAD4	chr4:48342451-48342749	H1-hESC	embryonic stem cell:	n/a	n/a
32	POLR2A	chr4:48342618-48344332	Hela-S3	cervix:	n/a	n/a
33	TBL1XR1	chr4:48342445-48343283	K562	blood:	n/a	n/a
34	TCF12	chr4:48342663-48343709	A549	lung:	n/a	n/a
35	MYC	chr4:48342602-48342758	MCF10A-Er-Src	breast:	n/a	n/a
36	POLR2A	chr4:48342340-48344634	GM12892	blood:	n/a	n/a
37	MTA3	chr4:48342359-48343293	GM12878	blood:	n/a	n/a
38	POLR2A	chr4:48342329-48344353	K562	blood:	n/a	n/a
39	FOXA1	chr4:48342492-48343358	HepG2	liver:	n/a	n/a
40	POLR2A	chr4:48342638-48342915	Hela-S3	cervix:	n/a	n/a
41	MYC	chr4:48342232-48344427	K562	blood:	n/a	n/a
42	FOXM1	chr4:48342416-48344211	GM12878	blood:	n/a	n/a
43	ELF1	chr4:48342643-48343670	K562	blood:	n/a	chr4:48342800-48342809 chr4:48343238-48343250
44	POLR2A	chr4:48342566-48344502	ProgFib	skin:	n/a	n/a
45	ATF2	chr4:48342661-48343686	GM12878	blood:	n/a	n/a
46	POLR2A	chr4:48342600-48344226	HEK293	kidney:	n/a	n/a
47	ZMIZ1	chr4:48342317-48343775	K562	blood:	n/a	n/a
48	POLR2A	chr4:48342299-48344339	MCF10A-Er-Src	breast:	n/a	n/a
49	POLR2A	chr4:48342486-48343818	K562	blood:	n/a	n/a
50	FOS	chr4:48342596-48343264	HUVEC	blood vessel:	n/a	chr4:48342747-48342758 chr4:48342726-48342735 chr4:48343239-48343248

No.	Distal block	Cell Line	Cell type
1	chr4:48342222..48343122-chr6:10417159..10417982,2	Hela-S3	cervix:
2	chr4:48341542..48343650-chr4:48378558..48381453,2	K562	blood:
3	chr4:48339667..48343042-chr4:48377720..48381453,4	K562	blood:
4	chr4:48270141..48273598-chr4:48341900..48344865,7	K562	blood:
5	chr4:48341515..48344236-chr4:48506268..48509029,2	K562	blood:
6	chr2:96873883..96874519-chr4:48342610..48343559,2	NB4	blood:
7	chr4:48341290..48343185-chr4:52708590..52710145,2	K562	blood:
8	chr4:48309394..48311856-chr4:48341157..48342687,2	K562	blood:
9	chr4:48270358..48273390-chr4:48340605..48344777,4	MCF-7	breast:
10	chr4:48269261..48273807-chr4:48342628..48344865,6	K562	blood:
11	chr4:48341909..48343469-chr4:48483589..48486077,2	K562	blood:
12	chr4:48312456..48314197-chr4:48341222..48342911,2	K562	blood:

Variant related genes	Relation type
SLAIN2	TF binding region
ENSG00000109171	Chromatin interaction
ENSG00000137203	Chromatin interaction
ENSG00000204685	Chromatin interaction
ENSG00000075539	Chromatin interaction
ENSG00000084090	Chromatin interaction
ENSG00000109184	Chromatin interaction
ENSG00000145248	Chromatin interaction
ENSG00000135605	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs13101954	0.80[AFR][1000 genomes]
rs13142082	0.80[AFR][1000 genomes]
rs1466631	0.80[AFR][1000 genomes]
rs1844149	0.80[AFR][1000 genomes]
rs2029347	0.80[AFR][1000 genomes]
rs2291476	0.80[AFR][1000 genomes]
rs28840724	0.80[AFR][1000 genomes]
rs384885	0.80[AFR][1000 genomes]
rs393338	0.80[AFR][1000 genomes]
rs397257	0.80[AFR][1000 genomes]
rs409911	0.80[AFR][1000 genomes]
rs4694894	0.80[AFR][1000 genomes]
rs4695374	0.80[AFR][1000 genomes]
rs565234	0.80[AFR][1000 genomes]
rs565385	0.80[AFR][1000 genomes]
rs62309450	0.80[AFR][1000 genomes]
rs66671150	0.92[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs6819696	0.80[AFR][1000 genomes]
rs6819847	0.80[AFR][1000 genomes]
rs73246023	0.80[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006610	chr4:48209294-48415387	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv537085	chr4:48209294-48415387	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	esv3377721	chr4:48342220-48345068	Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs56089943	SLC10A4	cis	lung	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48342000-48342800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
2	chr4:48342000-48342800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr4:48342000-48343000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
4	chr4:48342000-48343000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
5	chr4:48342000-48345400	Active TSS	ES-I3 Cell Line	embryonic stem cell
6	chr4:48342000-48345400	Active TSS	Fetal Intestine Large	intestine
7	chr4:48342000-48345600	Active TSS	Fetal Intestine Small	intestine
8	chr4:48342200-48342800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr4:48342200-48342800	Flanking Active TSS	A549	lung
10	chr4:48342200-48342800	Flanking Active TSS	Dnd41	blood
11	chr4:48342200-48342800	Flanking Active TSS	HSMM	muscle
12	chr4:48342200-48342800	Flanking Active TSS	HSMMtube	muscle
13	chr4:48342200-48342800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
14	chr4:48342200-48342800	Flanking Active TSS	NH-A	brain
15	chr4:48342200-48343000	Flanking Active TSS	HUVEC	blood vessel
16	chr4:48342200-48343000	Flanking Active TSS	NHEK	skin
17	chr4:48342200-48343200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr4:48342200-48343200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr4:48342200-48343200	Flanking Active TSS	GM12878-XiMat	blood
20	chr4:48342200-48343600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr4:48342200-48344200	Active TSS	Skeletal Muscle Female	skeletal muscle
22	chr4:48342200-48344400	Active TSS	Colonic Mucosa	Colon
23	chr4:48342200-48344600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
24	chr4:48342200-48345200	Active TSS	H9 Cell Line	embryonic stem cell
25	chr4:48342200-48345200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr4:48342200-48345200	Active TSS	HUES64 Cell Line	embryonic stem cell
27	chr4:48342200-48345200	Active TSS	Breast Myoepithelial Primary Cells	Breast
28	chr4:48342200-48345400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr4:48342200-48345400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr4:48342200-48345400	Active TSS	Brain Anterior Caudate	brain
31	chr4:48342200-48345600	Active TSS	H1 Cell Line	embryonic stem cell
32	chr4:48342200-48345800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr4:48342400-48342800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
34	chr4:48342400-48342800	Flanking Active TSS	Primary B cells from peripheral blood	blood
35	chr4:48342400-48342800	Flanking Active TSS	Primary T cells from cord blood	blood
36	chr4:48342400-48342800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
37	chr4:48342400-48342800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
38	chr4:48342400-48342800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
39	chr4:48342400-48342800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
40	chr4:48342400-48342800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr4:48342400-48342800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr4:48342400-48342800	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
43	chr4:48342400-48342800	Enhancers	Placenta Amnion	Placenta Amnion
44	chr4:48342400-48342800	Flanking Active TSS	Rectal Smooth Muscle	rectum
45	chr4:48342400-48342800	Enhancers	Spleen	Spleen
46	chr4:48342400-48343000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
47	chr4:48342400-48343000	Flanking Active TSS	Primary B cells from cord blood	blood
48	chr4:48342400-48343000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
49	chr4:48342400-48343000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
50	chr4:48342400-48343000	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood

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