Variant report

Variant	rs28538314
Chromosome Location	chr18:29671510-29671511
allele	G/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	POLR2A	chr18:29671489-29672893	PANC-1	pancreas:	n/a	n/a
2	MAFK	chr18:29671481-29672003	Hela-S3	cervix:	n/a	n/a
3	REST	chr18:29671472-29672999	HL-60	blood:	n/a	chr18:29672354-29672367 chr18:29671888-29671901
4	NRF1	chr18:29671500-29672064	GM12878	blood:	n/a	n/a
5	POLR2A	chr18:29671457-29673811	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr18:29671417-29673037	HUVEC	blood vessel:	n/a	n/a
7	HA-E2F1	chr18:29671449-29673562	MCF-7	breast:	n/a	chr18:29673118-29673125 chr18:29673118-29673125 chr18:29671985-29671994 chr18:29673118-29673125 chr18:29672983-29672998 chr18:29672596-29672605 chr18:29671983-29671993 chr18:29673117-29673129
8	MXI1	chr18:29671449-29673532	Hela-S3	cervix:	n/a	n/a
9	RCOR1	chr18:29671443-29672911	K562	blood:	n/a	n/a
10	POLR2A	chr18:29671450-29673005	PBDE	blood:	n/a	n/a
11	CREB1	chr18:29671452-29672923	K562	blood:	n/a	n/a
12	MAZ	chr18:29671509-29673826	K562	blood:	n/a	chr18:29672357-29672367 chr18:29672147-29672154 chr18:29672146-29672155 chr18:29672639-29672649
13	ZNF384	chr18:29671491-29672252	K562	blood:	n/a	n/a
14	POLR2A	chr18:29671475-29673078	HL-60	blood:	n/a	n/a
15	CREB1	chr18:29671504-29672179	K562	blood:	n/a	n/a
16	POLR2A	chr18:29671438-29673836	K562	blood:	n/a	n/a
17	POLR2A	chr18:29671407-29673805	GM12891	blood:	n/a	n/a
18	MAZ	chr18:29671415-29672887	GM12878	blood:	n/a	chr18:29672357-29672367 chr18:29672147-29672154 chr18:29671428-29671436 chr18:29672146-29672155 chr18:29672639-29672649
19	PML	chr18:29671385-29673081	GM12878	blood:	n/a	n/a
20	RUNX3	chr18:29671503-29672939	GM12878	blood:	n/a	n/a
21	HCFC1	chr18:29671246-29673672	Hela-S3	cervix:	n/a	n/a
22	MAX	chr18:29671469-29673374	ECC-1	luminal epithelium:	n/a	chr18:29672357-29672367 chr18:29672147-29672154 chr18:29672146-29672155 chr18:29672639-29672649
23	ATF2	chr18:29671493-29672135	GM12878	blood:	n/a	n/a
24	MXI1	chr18:29671260-29673910	SK-N-SH	brain:	n/a	n/a
25	TBL1XR1	chr18:29671498-29672046	K562	blood:	n/a	n/a
26	MAX	chr18:29671424-29673078	HCT-116	colon:	n/a	chr18:29672357-29672367 chr18:29672147-29672154 chr18:29671428-29671436 chr18:29672146-29672155 chr18:29672639-29672649
27	POLR2A	chr18:29671407-29673811	GM12878	blood:	n/a	n/a
28	CTCF	chr18:29671401-29671942	K562	blood:	n/a	n/a
29	BRCA1	chr18:29671503-29672004	Hela-S3	cervix:	n/a	n/a
30	POLR2A	chr18:29671497-29673114	PFSK-1	brain:	n/a	n/a
31	POLR2A	chr18:29671443-29673705	H1-hESC	embryonic stem cell:	n/a	n/a
32	POLR2A	chr18:29671506-29673651	GM12892	blood:	n/a	n/a
33	CREB1	chr18:29671404-29672936	H1-hESC	embryonic stem cell:	n/a	n/a
34	BCLAF1	chr18:29671454-29672193	GM12878	blood:	n/a	chr18:29671982-29671995 chr18:29671983-29671992
35	CREB1	chr18:29671495-29673075	GM12878	blood:	n/a	n/a
36	POLR2A	chr18:29671509-29673461	SK-N-MC	brain:	n/a	n/a
37	POLR2A	chr18:29671495-29673398	GM12892	blood:	n/a	n/a
38	USF2	chr18:29671465-29671882	Hela-S3	cervix:	n/a	n/a
39	TCF12	chr18:29671496-29672358	A549	lung:	n/a	n/a
40	REST	chr18:29671380-29673287	H1-neurons	neurons:	n/a	chr18:29672354-29672367 chr18:29671888-29671901
41	SIN3AK20	chr18:29671417-29673545	MCF-7	breast:	n/a	n/a
42	MTA3	chr18:29671330-29672392	GM12878	blood:	n/a	n/a
43	CREB1	chr18:29671482-29673196	HepG2	liver:	n/a	n/a
44	MAZ	chr18:29671510-29673867	IMR90	lung:	n/a	chr18:29672357-29672367 chr18:29672147-29672154 chr18:29672146-29672155 chr18:29672639-29672649
45	POLR2A	chr18:29671423-29673436	MCF10A-Er-Src	breast:	n/a	n/a
46	MAX	chr18:29671430-29673225	HCT-116	colon:	n/a	chr18:29672357-29672367 chr18:29672147-29672154 chr18:29672146-29672155 chr18:29672639-29672649
47	SP1	chr18:29671435-29673014	HCT-116	colon:	n/a	chr18:29672392-29672402 chr18:29672989-29672998 chr18:29672444-29672456 chr18:29672861-29672875 chr18:29672578-29672587 chr18:29672595-29672604 chr18:29672636-29672650 chr18:29672595-29672605 chr18:29672594-29672606 chr18:29672357-29672366 chr18:29672524-29672534 chr18:29672392-29672402 chr18:29671882-29671891 chr18:29672637-29672646 chr18:29672425-29672434 chr18:29672595-29672604 chr18:29671766-29671778 chr18:29672594-29672605 chr18:29671773-29671782 chr18:29672989-29672998 chr18:29672862-29672871 chr18:29672471-29672485 chr18:29672247-29672256 chr18:29672248-29672257 chr18:29672523-29672535 chr18:29672635-29672646 chr18:29672248-29672257 chr18:29672353-29672367 chr18:29672423-29672435 chr18:29672595-29672605 chr18:29672424-29672434 chr18:29672238-29672252 chr18:29672577-29672589 chr18:29672446-29672455 chr18:29671768-29671777 chr18:29672595-29672609 chr18:29672357-29672367 chr18:29672520-29672533 chr18:29671773-29671782 chr18:29672358-29672367 chr18:29672860-29672872 chr18:29672990-29672999 chr18:29672356-29672368 chr18:29672356-29672368 chr18:29672594-29672606 chr18:29672444-29672456 chr18:29672425-29672434 chr18:29672424-29672433 chr18:29672860-29672872 chr18:29671772-29671781 chr18:29672596-29672605 chr18:29672577-29672589 chr18:29672246-29672258 chr18:29671771-29671783
48	CTCF	chr18:29671485-29671544	Kidney_OC	kidney:	n/a	n/a
49	ARID3A	chr18:29671473-29672011	HepG2	liver:	n/a	n/a
50	RCOR1	chr18:29671424-29672512	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr18:29521939..29525237-chr18:29670716..29673913,4	MCF-7	breast:
2	chr18:29596689..29599956-chr18:29670764..29674475,6	MCF-7	breast:
3	chr18:29670755..29674701-chr18:29702072..29706406,4	K562	blood:
4	chr18:29671504..29673421-chr18:30049351..30052237,2	K562	blood:
5	chr18:29637884..29642506-chr18:29670649..29674281,4	K562	blood:
6	chr18:29597506..29599866-chr18:29670953..29673378,4	MCF-7	breast:
7	chr18:29521618..29525019-chr18:29670361..29672184,4	MCF-7	breast:
8	chr18:29654269..29657288-chr18:29670351..29673351,3	K562	blood:
9	chr18:29521537..29525393-chr18:29670839..29674328,7	K562	blood:
10	chr18:29520857..29524705-chr18:29670705..29674434,7	K562	blood:
11	chr18:29671417..29672347-chr20:42086520..42087354,2	Hela-S3	cervix:

Variant related genes	Relation type
ENSG00000238982	TF binding region
RNF138	TF binding region
ENSG00000134758	Chromatin interaction
ENSG00000265063	Chromatin interaction
ENSG00000263393	Chromatin interaction
ENSG00000153339	Chromatin interaction
ENSG00000101695	Chromatin interaction
ENSG00000214917	Chromatin interaction
ENSG00000141441	Chromatin interaction
ENSG00000263917	Chromatin interaction
ENSG00000263823	Chromatin interaction
ENSG00000124193	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11876397	1.00[MEX][hapmap]
rs16962691	1.00[YRI][hapmap]
rs28376309	1.00[AMR][1000 genomes]
rs28429168	1.00[AMR][1000 genomes]
rs28464735	1.00[AMR][1000 genomes]
rs28478378	1.00[AMR][1000 genomes]
rs28505817	1.00[AMR][1000 genomes]
rs28556958	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28596473	1.00[AMR][1000 genomes]
rs28727388	1.00[AMR][1000 genomes]
rs28822754	1.00[AMR][1000 genomes]
rs7239030	1.00[AMR][1000 genomes]
rs73413957	1.00[AMR][1000 genomes]
rs73413961	1.00[AMR][1000 genomes]
rs8091726	1.00[ASW][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs9949793	0.87[YRI][hapmap];1.00[AMR][1000 genomes]
rs9951329	1.00[MEX][hapmap]
rs9954827	1.00[AMR][1000 genomes]
rs9954966	1.00[AMR][1000 genomes]
rs9963611	1.00[AMR][1000 genomes]
rs9967305	1.00[YRI][hapmap];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757673	chr18:29632749-29674992	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	esv2758719	chr18:29632749-29674992	Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv909521	chr18:29645496-29671510	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv909522	chr18:29645496-29674992	Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv909523	chr18:29645496-29679922	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
6	nsv1055457	chr18:29654978-29677371	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:29664600-29671600	Weak transcription	Left Ventricle	heart
2	chr18:29665200-29671800	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr18:29667200-29671600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr18:29667200-29671600	Weak transcription	Stomach Mucosa	stomach
5	chr18:29667600-29671600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr18:29671000-29671600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
7	chr18:29671200-29671600	Enhancers	Primary T helper cells fromperipheralblood	blood
8	chr18:29671200-29672400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr18:29671200-29673800	Active TSS	H1 Cell Line	embryonic stem cell
10	chr18:29671200-29674000	Active TSS	HUES48 Cell Line	embryonic stem cell
11	chr18:29671200-29675000	Active TSS	GM12878-XiMat	blood
12	chr18:29671400-29671600	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
13	chr18:29671400-29671600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr18:29671400-29671600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr18:29671400-29671600	Flanking Active TSS	Primary T cells from cord blood	blood
16	chr18:29671400-29671600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
17	chr18:29671400-29671600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
18	chr18:29671400-29671600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
19	chr18:29671400-29671600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
20	chr18:29671400-29671600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr18:29671400-29671600	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
22	chr18:29671400-29671600	Enhancers	Cortex derived primary cultured neurospheres	brain
23	chr18:29671400-29671600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr18:29671400-29671600	Flanking Active TSS	Brain Germinal Matrix	brain
25	chr18:29671400-29671600	Flanking Active TSS	Brain Substantia Nigra	brain
26	chr18:29671400-29671600	Flanking Active TSS	Fetal Brain Female	brain
27	chr18:29671400-29671600	Flanking Active TSS	Fetal Intestine Large	intestine
28	chr18:29671400-29671600	Flanking Active TSS	Fetal Kidney	kidney
29	chr18:29671400-29671600	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
30	chr18:29671400-29671600	Flanking Active TSS	Fetal Lung	lung
31	chr18:29671400-29671600	Active TSS	Fetal Muscle Trunk	muscle
32	chr18:29671400-29671600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
33	chr18:29671400-29671600	Flanking Active TSS	Rectal Smooth Muscle	rectum
34	chr18:29671400-29671600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
35	chr18:29671400-29671600	Active TSS	Stomach Smooth Muscle	stomach
36	chr18:29671400-29671600	Flanking Active TSS	HSMM	muscle
37	chr18:29671400-29671600	Flanking Active TSS	K562	blood
38	chr18:29671400-29671600	Flanking Active TSS	NHLF	lung
39	chr18:29671400-29671800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr18:29671400-29671800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
41	chr18:29671400-29671800	Flanking Active TSS	Primary B cells from peripheral blood	blood
42	chr18:29671400-29671800	Flanking Active TSS	Primary hematopoietic stem cells	blood
43	chr18:29671400-29671800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
44	chr18:29671400-29671800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
45	chr18:29671400-29671800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
46	chr18:29671400-29671800	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
47	chr18:29671400-29671800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
48	chr18:29671400-29671800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr18:29671400-29671800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr18:29671400-29671800	Flanking Active TSS	Muscle Satellite Cultured Cells	--

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