Variant report

Variant	rs6023036
Chromosome Location	chr20:52824127-52824128
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	REST	chr20:52824043-52825584	H1-neurons	neurons:	n/a	chr20:52825302-52825312 chr20:52825295-52825308
2	MAX	chr20:52824117-52825206	SK-N-SH	brain:	n/a	n/a
3	FOXA1	chr20:52824123-52824810	HepG2	liver:	n/a	n/a
4	MAX	chr20:52824084-52825514	HCT-116	colon:	n/a	n/a
5	MEF2A	chr20:52824114-52825044	SK-N-SH	brain:	n/a	n/a
6	TCF7L2	chr20:52823981-52824783	MCF-7	breast:	n/a	chr20:52824304-52824313 chr20:52824302-52824316 chr20:52824305-52824315 chr20:52824301-52824317 chr20:52824302-52824316 chr20:52824301-52824317
7	NFIC	chr20:52824120-52824788	HepG2	liver:	n/a	n/a
8	FOXA1	chr20:52824126-52824816	HepG2	liver:	n/a	n/a
9	TCF7L2	chr20:52824022-52825283	Hela-S3	cervix:	n/a	chr20:52824304-52824313 chr20:52824302-52824316 chr20:52824305-52824315 chr20:52824301-52824317 chr20:52824302-52824316 chr20:52824301-52824317
10	TEAD4	chr20:52824018-52824696	HepG2	liver:	n/a	n/a
11	TCF12	chr20:52824112-52824746	ECC-1	luminal epithelium:	n/a	n/a
12	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
13	HCFC1	chr20:52823925-52826039	Hela-S3	cervix:	n/a	n/a
14	YY1	chr20:52824125-52825031	HepG2	liver:	n/a	chr20:52824635-52824647 chr20:52824364-52824378 chr20:52824696-52824705 chr20:52824610-52824619 chr20:52824347-52824361
15	TEAD4	chr20:52823819-52825599	A549	lung:	n/a	n/a
16	BCLAF1	chr20:52824074-52824816	GM12878	blood:	n/a	chr20:52824366-52824379 chr20:52824365-52824378 chr20:52824363-52824376
17	GATA3	chr20:52824104-52825036	A549	lung:	n/a	chr20:52824149-52824162
18	CTCF	chr20:52824096-52824523	A549	lung:	n/a	chr20:52824351-52824364 chr20:52824349-52824367 chr20:52824352-52824362 chr20:52824350-52824366
19	PBX3	chr20:52824123-52824744	A549	lung:	n/a	n/a
20	MBD4	chr20:52823969-52824822	HepG2	liver:	n/a	n/a
21	ATF3	chr20:52824089-52824598	A549	lung:	n/a	n/a
22	EP300	chr20:52824096-52824784	A549	lung:	n/a	chr20:52824696-52824705 chr20:52824358-52824374 chr20:52824357-52824373
23	MYBL2	chr20:52823764-52825510	HepG2	liver:	n/a	chr20:52825310-52825324
24	CTCF	chr20:52823773-52824850	A549	lung:	n/a	chr20:52824351-52824364 chr20:52824349-52824367 chr20:52824352-52824362 chr20:52824350-52824366
25	BCL3	chr20:52824084-52824744	A549	lung:	n/a	chr20:52824366-52824379 chr20:52824365-52824378 chr20:52824363-52824376
26	TCF7L2	chr20:52824008-52824542	HepG2	liver:	n/a	chr20:52824304-52824313 chr20:52824302-52824316 chr20:52824305-52824315 chr20:52824301-52824317 chr20:52824302-52824316 chr20:52824301-52824317
27	MAX	chr20:52824062-52825175	A549	lung:	n/a	n/a
28	MAX	chr20:52824125-52825313	ECC-1	luminal epithelium:	n/a	n/a
29	TCF12	chr20:52823966-52825629	A549	lung:	n/a	n/a
30	BCLAF1	chr20:52824106-52824660	GM12878	blood:	n/a	chr20:52824366-52824379 chr20:52824365-52824378 chr20:52824363-52824376
31	GATA3	chr20:52824122-52824672	T-47D	breast:	n/a	chr20:52824149-52824162
32	CTCF	chr20:52823777-52825261	SK-N-SH	brain:	n/a	chr20:52824351-52824364 chr20:52824349-52824367 chr20:52824352-52824362 chr20:52824350-52824366
33	SP1	chr20:52824066-52824893	A549	lung:	n/a	chr20:52824383-52824393 chr20:52824383-52824393
34	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
35	MAX	chr20:52824052-52825752	HepG2	liver:	n/a	n/a
36	SP1	chr20:52824071-52824847	A549	lung:	n/a	chr20:52824383-52824393 chr20:52824383-52824393
37	SIX5	chr20:52824017-52824802	A549	lung:	n/a	n/a
38	SREBP1	chr20:52823946-52825033	GM12878	blood:	n/a	n/a
39	CTCF	chr20:52824116-52824861	IMR90	lung:	n/a	chr20:52824351-52824364 chr20:52824349-52824367 chr20:52824352-52824362 chr20:52824350-52824366
40	REST	chr20:52823970-52825140	A549	lung:	n/a	n/a
41	ESRRA	chr20:52823794-52824987	GM12878	blood:	n/a	n/a
42	EP300	chr20:52824068-52824701	HepG2	liver:	n/a	chr20:52824358-52824374 chr20:52824357-52824373
43	MTA3	chr20:52824123-52824726	GM12878	blood:	n/a	n/a
44	JUND	chr20:52824008-52825751	SK-N-SH	brain:	n/a	chr20:52824756-52824770
45	JUND	chr20:52824021-52824979	GM12878	blood:	n/a	chr20:52824756-52824770
46	RAD21	chr20:52824121-52824616	ECC-1	luminal epithelium:	n/a	chr20:52824351-52824365 chr20:52824360-52824373 chr20:52824351-52824361 chr20:52824350-52824363
47	HDAC2	chr20:52824073-52824876	HepG2	liver:	n/a	n/a
48	HDAC2	chr20:52824108-52824560	H1-hESC	embryonic stem cell:	n/a	n/a
49	MAX	chr20:52823650-52828561	MCF-7	breast:	n/a	chr20:52826819-52826828
50	TCF7L2	chr20:52823945-52824721	PANC-1	pancreas:	n/a	chr20:52824304-52824313 chr20:52824302-52824316 chr20:52824305-52824315 chr20:52824301-52824317 chr20:52824302-52824316 chr20:52824301-52824317

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr20:52824106-52824156	HUVEC	blood vessel:	n/a
2	chr20:52824106-52824156	HEK293	kidney:	embryo
3	chr20:52824106-52824156	NH-A	brain:	n/a
4	chr20:52824106-52824156	HCPEpiC	choroid plexus:	n/a
5	chr20:52824106-52824156	GM12892	blood:	n/a
6	chr20:52824106-52824156	T-47D	breast:	n/a
7	chr20:52824106-52824156	PrEC	prostate:	n/a
8	chr20:52824106-52824156	HMEC	breast:	n/a
9	chr20:52824106-52824156	AG09309	skin:	n/a
10	chr20:52824106-52824156	AG04450	lung:	fetal
11	chr20:52824106-52824156	HCM	heart:	n/a
12	chr20:52824106-52824156	BE2_C	brain:	n/a
13	chr20:52824106-52824156	K562	blood:	n/a
14	chr20:52824106-52824156	MCF10A-Er-Src	breast:	n/a
15	chr20:52824106-52824156	IMR90	lung:	fetal
16	chr20:52824106-52824156	A549	lung:	n/a
17	chr20:52824106-52824156	HCT-116	colon:	n/a
18	chr20:52824106-52824156	HAEpiC	amniotic membrane:	n/a
19	chr20:52824106-52824156	SKMC	muscle:	n/a
20	chr20:52824106-52824156	HL-60	blood:	n/a
21	chr20:52824106-52824156	ovcar-3	ovarian:	n/a
22	chr20:52824106-52824156	HRCEpiC	kidney:	n/a
23	chr20:52824106-52824156	NHDF-neo	bronchial:	n/a
24	chr20:52824106-52824156	SK-N-SH_RA	brain:	n/a
25	chr20:52824106-52824156	LNCaP	prostate:	n/a
26	chr20:52824106-52824156	Caco-2	colon:	n/a
27	chr20:52824106-52824156	HNPCEpiC	eye:	n/a
28	chr20:52824106-52824156	HPAEpiC	pulmonary alveolar:	n/a
29	chr20:52824106-52824156	ProgFib	skin:	n/a
30	chr20:52824106-52824156	GM06990	blood:	n/a
31	chr20:52824106-52824156	H1-hESC	embryonic stem cell:	embryo
32	chr20:52824106-52824156	AG10803	skin:	n/a
33	chr20:52824106-52824156	HIPEpiC	eye:	n/a
34	chr20:52824106-52824156	RPTEC	kidney:	n/a
35	chr20:52824106-52824156	SK-N-SH	brain:	n/a
36	chr20:52824106-52824156	NHBE	bronchial:	n/a
37	chr20:52824106-52824156	Jurkat	blood:	n/a
38	chr20:52824106-52824156	U87	brain:	n/a
39	chr20:52824106-52824156	ECC-1	luminal epithelium:	n/a
40	chr20:52824106-52824156	HEEpiC	esophagus:	n/a
41	chr20:52824106-52824156	AoSMC	blood vessel:	n/a
42	chr20:52824106-52824156	GM12891	blood:	n/a
43	chr20:52824106-52824156	HepG2	liver:	n/a
44	chr20:52824106-52824156	AG09319	gingival:	n/a
45	chr20:52824106-52824156	CMK	blood:	n/a
46	chr20:52824106-52824156	NT2-D1	testis:	n/a
47	chr20:52824106-52824156	Hepatocyte	liver:	n/a
48	chr20:52824106-52824156	AG04449	skin:	fetal
49	chr20:52824106-52824156	MCF-7	breast:	n/a
50	chr20:52824106-52824156	PFSK-1	brain:	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	chr2:24427506..24429704-chr20:52824121..52825744,2	MCF-7	breast:
7	chr17:56707891..56709525-chr20:52823914..52825675,2	MCF-7	breast:
8	chr20:52823050..52825968-chr20:55840171..55842066,3	MCF-7	breast:
9	chr20:52824010..52825675-chr3:4920245..4923107,2	MCF-7	breast:
10	chr14:65877799..65879344-chr20:52823519..52825312,2	MCF-7	breast:
11	chr20:46413701..46416832-chr20:52824005..52826708,3	MCF-7	breast:
12	chr20:52209344..52211944-chr20:52823428..52825795,3	MCF-7	breast:
13	chr16:30996907..30999172-chr20:52823827..52825691,2	MCF-7	breast:
14	chr17:56707871..56710352-chr20:52821749..52824692,2	MCF-7	breast:
15	chr20:46414954..46415490-chr20:52823892..52824588,3	MCF-7	breast:
16	chr20:52822868..52824731-chr3:63848647..63850242,2	MCF-7	breast:
17	chr12:122238562..122240078-chr20:52823765..52826004,2	MCF-7	breast:
18	chr17:56735044..56737047-chr20:52822984..52826992,5	MCF-7	breast:
19	chr17:58752920..58755421-chr20:52823131..52825781,2	MCF-7	breast:
20	chr20:52815607..52816606-chr20:52823726..52824376,2	K562	blood:
21	chr1:101359870..101360622-chr20:52823968..52824887,2	Hela-S3	cervix:

Variant related genes	Relation type
PFDN4	TF binding region
PFDN4	CpG island
ENSG00000163634	Chromatin interaction
ENSG00000198399	Chromatin interaction
ENSG00000273204	Chromatin interaction
ENSG00000212195	Chromatin interaction
ENSG00000226308	Chromatin interaction
ENSG00000196562	Chromatin interaction
ENSG00000139725	Chromatin interaction
ENSG00000202077	Chromatin interaction
ENSG00000033170	Chromatin interaction
ENSG00000169242	Chromatin interaction
ENSG00000254290	Chromatin interaction
ENSG00000225563	Chromatin interaction
ENSG00000212694	Chromatin interaction
ENSG00000163635	Chromatin interaction
ENSG00000141376	Chromatin interaction
ENSG00000162694	Chromatin interaction
ENSG00000200972	Chromatin interaction
ENSG00000268863	Chromatin interaction
ENSG00000101144	Chromatin interaction
ENSG00000124171	Chromatin interaction
ENSG00000239126	Chromatin interaction
ENSG00000171940	Chromatin interaction

Extended variants
information (count: 4 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs6097840	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6097841	0.91[AFR][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:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52811400-52824200	Weak transcription	Right Atrium	heart
2	chr20:52818000-52824200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr20:52818000-52824400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr20:52818200-52824200	Weak transcription	Colonic Mucosa	Colon
5	chr20:52819000-52824200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr20:52820200-52824200	Weak transcription	Spleen	Spleen
7	chr20:52820400-52824200	Weak transcription	Monocytes-CD14+_RO01746	blood
8	chr20:52821000-52824200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr20:52821000-52824400	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr20:52821800-52824200	Weak transcription	HMEC	breast
11	chr20:52823800-52824200	Enhancers	Right Ventricle	heart
12	chr20:52823800-52824400	Enhancers	Rectal Mucosa Donor 31	rectum
13	chr20:52823800-52825000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr20:52824000-52824200	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr20:52824000-52824200	Enhancers	Primary B cells from peripheral blood	blood
16	chr20:52824000-52824200	Enhancers	Primary T helper cells fromperipheralblood	blood
17	chr20:52824000-52824200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr20:52824000-52824200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
19	chr20:52824000-52824200	Enhancers	Adipose Nuclei	Adipose
20	chr20:52824000-52824200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
21	chr20:52824000-52824200	Enhancers	Stomach Smooth Muscle	stomach
22	chr20:52824000-52824200	Flanking Bivalent TSS/Enh	HepG2	liver
23	chr20:52824000-52824400	Enhancers	Primary monocytes fromperipheralblood	blood
24	chr20:52824000-52824400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr20:52824000-52824400	Enhancers	Fetal Intestine Large	intestine
26	chr20:52824000-52824400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
27	chr20:52824000-52824400	Flanking Active TSS	Dnd41	blood
28	chr20:52824000-52824400	Flanking Active TSS	GM12878-XiMat	blood
29	chr20:52824000-52824600	Active TSS	Primary B cells from cord blood	blood
30	chr20:52824000-52824600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
31	chr20:52824000-52824800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr20:52824000-52824800	Active TSS	Skeletal Muscle Female	skeletal muscle
33	chr20:52824000-52825000	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
34	chr20:52824000-52825000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr20:52824000-52825000	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr20:52824000-52825200	Active TSS	Primary T cells from cord blood	blood
37	chr20:52824000-52825200	Active TSS	Brain Germinal Matrix	brain
38	chr20:52824000-52825200	Active TSS	Duodenum Mucosa	Duodenum
39	chr20:52824000-52825400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr20:52824000-52825400	Active TSS	Primary T helper cells PMA-I stimulated	--
41	chr20:52824000-52825400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr20:52824000-52825400	Active TSS	Brain Angular Gyrus	brain
43	chr20:52824000-52825400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
44	chr20:52824000-52825400	Active TSS	Skeletal Muscle Male	skeletal muscle
45	chr20:52824000-52825400	Active TSS	Hela-S3	cervix
46	chr20:52824000-52825400	Active TSS	NHEK	skin
47	chr20:52824000-52825400	Active TSS	Osteobl	bone
48	chr20:52824000-52825600	Active TSS	iPS-20b Cell Line	embryonic stem cell
49	chr20:52824000-52825600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr20:52824000-52825600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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