Variant report

Variant	rs6097840
Chromosome Location	chr20:52823939-52823940
allele	A/G
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	CTCF	chr20:52823900-52824050	GM12801	blood:	n/a	n/a
2	TCF7L2	chr20:52823682-52824660	HEK293	kidney:	n/a	chr20:52824304-52824313 chr20:52824302-52824316 chr20:52824305-52824315 chr20:52824301-52824317 chr20:52824302-52824316 chr20:52824301-52824317
3	HCFC1	chr20:52823925-52826039	Hela-S3	cervix:	n/a	n/a
4	TEAD4	chr20:52823819-52825599	A549	lung:	n/a	n/a
5	CTCF	chr20:52823920-52824070	GM12872	blood:	n/a	n/a
6	MYBL2	chr20:52823764-52825510	HepG2	liver:	n/a	chr20:52825310-52825324
7	CTCF	chr20:52823773-52824850	A549	lung:	n/a	chr20:52824351-52824364 chr20:52824349-52824367 chr20:52824352-52824362 chr20:52824350-52824366
8	CTCF	chr20:52823777-52825261	SK-N-SH	brain:	n/a	chr20:52824351-52824364 chr20:52824349-52824367 chr20:52824352-52824362 chr20:52824350-52824366
9	TCF7L2	chr20:52823915-52824796	HCT-116	colon:	n/a	chr20:52824304-52824313 chr20:52824302-52824316 chr20:52824305-52824315 chr20:52824301-52824317 chr20:52824302-52824316 chr20:52824301-52824317
10	ESRRA	chr20:52823794-52824987	GM12878	blood:	n/a	n/a
11	CTCF	chr20:52823840-52823990	HEEpiC	esophagus:	n/a	n/a
12	CTCF	chr20:52823900-52824050	HCPEpiC	choroid plexus:	n/a	n/a
13	MAX	chr20:52823650-52828561	MCF-7	breast:	n/a	chr20:52826819-52826828
14	CHD1	chr20:52823868-52825544	IMR90	lung:	n/a	chr20:52824817-52824827
15	MAX	chr20:52823808-52825547	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:210544901..210547632-chr20:52822765..52825018,2	MCF-7	breast:
2	chr20:49345330..49348251-chr20:52823191..52827147,4	MCF-7	breast:
3	chr1:155099597..155102197-chr20:52823453..52826190,2	MCF-7	breast:
4	chr20:52417422..52419776-chr20:52823740..52825810,2	MCF-7	breast:
5	chr20:52823530..52825311-chr8:37457254..37459183,2	MCF-7	breast:
6	chr17:56707891..56709525-chr20:52823914..52825675,2	MCF-7	breast:
7	chr20:52823050..52825968-chr20:55840171..55842066,3	MCF-7	breast:
8	chr14:65877799..65879344-chr20:52823519..52825312,2	MCF-7	breast:
9	chr20:52209344..52211944-chr20:52823428..52825795,3	MCF-7	breast:
10	chr16:30996907..30999172-chr20:52823827..52825691,2	MCF-7	breast:
11	chr17:56707871..56710352-chr20:52821749..52824692,2	MCF-7	breast:
12	chr20:46414954..46415490-chr20:52823892..52824588,3	MCF-7	breast:
13	chr20:52822868..52824731-chr3:63848647..63850242,2	MCF-7	breast:
14	chr12:122238562..122240078-chr20:52823765..52826004,2	MCF-7	breast:
15	chr17:56735044..56737047-chr20:52822984..52826992,5	MCF-7	breast:
16	chr17:58752920..58755421-chr20:52823131..52825781,2	MCF-7	breast:
17	chr20:52815607..52816606-chr20:52823726..52824376,2	K562	blood:

Variant related genes	Relation type
PFDN4	TF binding region
ENSG00000124171	Chromatin interaction
ENSG00000171940	Chromatin interaction
ENSG00000202077	Chromatin interaction
ENSG00000101144	Chromatin interaction
ENSG00000169242	Chromatin interaction
ENSG00000212195	Chromatin interaction
ENSG00000226308	Chromatin interaction
ENSG00000033170	Chromatin interaction
ENSG00000254290	Chromatin interaction
ENSG00000200972	Chromatin interaction
ENSG00000225563	Chromatin interaction
ENSG00000212694	Chromatin interaction
ENSG00000196562	Chromatin interaction
ENSG00000268863	Chromatin interaction
ENSG00000139725	Chromatin interaction
ENSG00000163634	Chromatin interaction
ENSG00000141376	Chromatin interaction
ENSG00000163635	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs6013926	0.83[TSI][hapmap]
rs6013930	1.00[TSI][hapmap]
rs6023036	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6097841	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv586224	chr20:52474850-53279490	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	338 gene(s)	inside rSNPs	diseases
2	nsv834010	chr20:52759824-52932939	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS 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	119 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52811400-52824200	Weak transcription	Right Atrium	heart
2	chr20:52818000-52824000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr20:52818000-52824200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr20:52818000-52824400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr20:52818200-52824200	Weak transcription	Colonic Mucosa	Colon
6	chr20:52819000-52824200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr20:52820200-52824200	Weak transcription	Spleen	Spleen
8	chr20:52820400-52824200	Weak transcription	Monocytes-CD14+_RO01746	blood
9	chr20:52820800-52824000	Weak transcription	Primary monocytes fromperipheralblood	blood
10	chr20:52820800-52824000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr20:52821000-52824200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr20:52821000-52824400	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr20:52821200-52824000	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr20:52821800-52824200	Weak transcription	HMEC	breast
15	chr20:52822600-52824000	Enhancers	GM12878-XiMat	blood
16	chr20:52823000-52824000	Weak transcription	K562	blood
17	chr20:52823800-52824000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr20:52823800-52824000	Bivalent Enhancer	HepG2	liver
19	chr20:52823800-52824200	Enhancers	Right Ventricle	heart
20	chr20:52823800-52824400	Enhancers	Rectal Mucosa Donor 31	rectum
21	chr20:52823800-52825000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood

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