Variant report

Variant	rs67546863
Chromosome Location	chr3:136471914-136471915
allele	C/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	chr3:136471900-136472050	AoAF	blood vessel:	n/a	n/a
2	SMC3	chr3:136469791-136472601	Hela-S3	cervix:	n/a	chr3:136471189-136471203 chr3:136470573-136470583 chr3:136471247-136471261 chr3:136471196-136471203
3	CTCF	chr3:136469715-136472254	A549	lung:	n/a	chr3:136471189-136471202 chr3:136471247-136471260 chr3:136471240-136471261 chr3:136471189-136471202 chr3:136471187-136471205 chr3:136471511-136471524 chr3:136471246-136471262 chr3:136471188-136471204 chr3:136471245-136471263 chr3:136471182-136471203 chr3:136471682-136471695 chr3:136471190-136471200
4	RFX5	chr3:136471069-136471988	HepG2	liver:	n/a	n/a
5	TAL1	chr3:136469847-136472703	K562	blood:	n/a	chr3:136471188-136471203 chr3:136471188-136471203 chr3:136471188-136471203
6	CTCF	chr3:136471820-136471970	A549	lung:	n/a	n/a
7	MYC	chr3:136469913-136472218	K562	blood:	n/a	chr3:136470730-136470740 chr3:136470527-136470536 chr3:136470260-136470270 chr3:136471424-136471434
8	RAD21	chr3:136471020-136472427	GM12878	blood:	n/a	chr3:136471510-136471523 chr3:136471185-136471204 chr3:136471188-136471201 chr3:136471511-136471525 chr3:136471245-136471257 chr3:136471189-136471203 chr3:136471513-136471527 chr3:136471247-136471261 chr3:136471243-136471262
9	CTCF	chr3:136471900-136472050	HEEpiC	esophagus:	n/a	n/a
10	TAF1	chr3:136470602-136472145	ECC-1	luminal epithelium:	n/a	n/a
11	CTCF	chr3:136471840-136471990	GM12867	blood:	n/a	n/a
12	CTCF	chr3:136471852-136472063	Gliobla	brain:	n/a	n/a
13	IRF1	chr3:136470892-136472301	K562	blood:	n/a	chr3:136472253-136472265 chr3:136471419-136471433 chr3:136472122-136472132 chr3:136471454-136471463 chr3:136472253-136472265
14	SMC3	chr3:136470987-136472115	K562	blood:	n/a	chr3:136471189-136471203 chr3:136471247-136471261 chr3:136471196-136471203
15	TEAD4	chr3:136471605-136472140	HepG2	liver:	n/a	n/a
16	CHD2	chr3:136470800-136472196	GM12878	blood:	n/a	n/a
17	MXI1	chr3:136470163-136472420	HepG2	liver:	n/a	chr3:136472194-136472203
18	POLR2A	chr3:136471004-136472208	K562	blood:	n/a	n/a
19	RAD21	chr3:136470693-136472375	HCT-116	colon:	n/a	chr3:136471510-136471523 chr3:136471185-136471204 chr3:136471188-136471201 chr3:136471511-136471525 chr3:136471245-136471257 chr3:136471189-136471203 chr3:136471513-136471527 chr3:136471247-136471261 chr3:136471243-136471262 chr3:136470751-136470764
20	POLR2A	chr3:136470033-136472148	K562	blood:	n/a	n/a
21	CTCF	chr3:136471909-136472003	GM13976	blood:	n/a	n/a
22	TCF7L2	chr3:136471179-136472095	Hela-S3	cervix:	n/a	n/a
23	TBP	chr3:136471193-136472464	GM12878	blood:	n/a	n/a
24	CTCF	chr3:136471820-136471970	Caco-2	colon:	n/a	n/a
25	POLR2A	chr3:136468906-136472752	PBDE	blood:	n/a	n/a
26	POU2F2	chr3:136471475-136472167	GM12891	blood:	n/a	chr3:136471961-136471974 chr3:136471963-136471972
27	YY1	chr3:136470561-136472076	SK-N-SH	brain:	n/a	chr3:136470937-136470954 chr3:136471574-136471590 chr3:136470939-136470949 chr3:136470758-136470769 chr3:136471423-136471432 chr3:136471575-136471585 chr3:136470939-136470961 chr3:136471052-136471061 chr3:136471575-136471585 chr3:136471546-136471560 chr3:136471418-136471432 chr3:136471337-136471348 chr3:136471189-136471197 chr3:136471573-136471590
28	RAD21	chr3:136471015-136472693	Hela-S3	cervix:	n/a	chr3:136471510-136471523 chr3:136471185-136471204 chr3:136471188-136471201 chr3:136471511-136471525 chr3:136471245-136471257 chr3:136471189-136471203 chr3:136471513-136471527 chr3:136471247-136471261 chr3:136471243-136471262
29	CTCF	chr3:136470924-136472161	IMR90	lung:	n/a	chr3:136471189-136471202 chr3:136471247-136471260 chr3:136471240-136471261 chr3:136471189-136471202 chr3:136471187-136471205 chr3:136471511-136471524 chr3:136471246-136471262 chr3:136471188-136471204 chr3:136471245-136471263 chr3:136471182-136471203 chr3:136471682-136471695 chr3:136471190-136471200
30	CTCF	chr3:136471780-136471930	Hela-S3	cervix:	n/a	n/a
31	RAD21	chr3:136470669-136472252	HCT-116	colon:	n/a	chr3:136471510-136471523 chr3:136471185-136471204 chr3:136471188-136471201 chr3:136471511-136471525 chr3:136471245-136471257 chr3:136471189-136471203 chr3:136471513-136471527 chr3:136471247-136471261 chr3:136471243-136471262 chr3:136470751-136470764
32	CTCF	chr3:136471860-136472010	HAc	cerebellar:	n/a	n/a
33	CTCF	chr3:136471860-136472010	GM12871	blood:	n/a	n/a
34	IRF1	chr3:136471135-136472380	K562	blood:	n/a	chr3:136472253-136472265 chr3:136471419-136471433 chr3:136472122-136472132 chr3:136471454-136471463 chr3:136472253-136472265
35	POLR2A	chr3:136470008-136472743	K562	blood:	n/a	n/a
36	NRF1	chr3:136471132-136472080	GM12878	blood:	n/a	chr3:136471376-136471385 chr3:136471423-136471432 chr3:136471543-136471554 chr3:136471545-136471554 chr3:136471376-136471390 chr3:136471439-136471450 chr3:136471373-136471387 chr3:136471376-136471387
37	YY1	chr3:136470746-136471961	K562	blood:	n/a	chr3:136470937-136470954 chr3:136471574-136471590 chr3:136470939-136470949 chr3:136470758-136470769 chr3:136471423-136471432 chr3:136471575-136471585 chr3:136470939-136470961 chr3:136471052-136471061 chr3:136471575-136471585 chr3:136471546-136471560 chr3:136471418-136471432 chr3:136471337-136471348 chr3:136471189-136471197 chr3:136471573-136471590
38	CREB1	chr3:136470864-136472278	GM12878	blood:	n/a	n/a
39	CTCF	chr3:136471818-136472073	SK-N-SH_RA	brain:	n/a	n/a
40	POLR2A	chr3:136470068-136472074	K562	blood:	n/a	n/a
41	POLR2A	chr3:136470364-136471922	HepG2	liver:	n/a	n/a
42	RELA	chr3:136471061-136472374	GM19193	blood:	n/a	n/a
43	FOS	chr3:136471874-136472086	MCF10A-Er-Src	breast:	n/a	n/a
44	ATF2	chr3:136470994-136472378	GM12878	blood:	n/a	n/a
45	TBL1XR1	chr3:136471165-136471996	K562	blood:	n/a	n/a
46	CTCF	chr3:136471881-136472044	GM10248	blood:	n/a	n/a
47	NFATC1	chr3:136471521-136472145	GM12878	blood:	n/a	n/a
48	MXI1	chr3:136470232-136472215	GM12878	blood:	n/a	chr3:136472194-136472203
49	MAX	chr3:136471819-136472507	H1-hESC	embryonic stem cell:	n/a	n/a
50	CTCF	chr3:136471878-136472051	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:136466613..136474326-chr3:136579481..136583133,10	K562	blood:
2	chr3:136471576..136472305-chr3:136732784..136733377,2	MCF-7	breast:
3	chr12:7053185..7053691-chr3:136471368..136471965,2	Hela-S3	cervix:
4	chr3:136470318..136472005-chr3:161088059..161090755,2	MCF-7	breast:
5	chr3:136471382..136472078-chr9:98079172..98080015,2	HCT-116	colon:
6	chr3:136453394..136456450-chr3:136469548..136472199,3	K562	blood:
7	chr3:136471389..136473293-chr3:136580852..136582413,2	MCF-7	breast:
8	chr3:135968107..135969967-chr3:136470513..136472370,2	MCF-7	breast:
9	chr3:136468701..136475672-chr3:136535815..136540749,9	K562	blood:
10	chr3:136350170..136353597-chr3:136468835..136472616,3	MCF-7	breast:
11	chr3:135968756..135970580-chr3:136469634..136471998,2	K562	blood:
12	chr3:135912902..135916874-chr3:136469598..136473232,8	MCF-7	breast:
13	chr3:135914989..135917015-chr3:136470237..136472481,3	K562	blood:
14	chr3:136469311..136474326-chr3:136579207..136583133,7	K562	blood:
15	chr3:135912817..135916962-chr3:136469681..136473212,8	K562	blood:
16	chr3:136277326..136280102-chr3:136471685..136473348,2	MCF-7	breast:
17	chr3:135967505..135970256-chr3:136469769..136472442,3	K562	blood:
18	chr3:135969104..135971090-chr3:136470031..136473091,3	MCF-7	breast:
19	chr3:136469358..136473351-chr3:136579831..136582888,9	MCF-7	breast:
20	chr3:136471501..136472073-chr7:6143796..6144617,2	Hela-S3	cervix:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TMEM22-1	chr3:136471472-136474622	ENSG00000261758.1

Variant related genes	Relation type
STAG1	TF binding region
ENSG00000106346	Chromatin interaction
ENSG00000174579	Chromatin interaction
ENSG00000111678	Chromatin interaction
ENSG00000114054	Chromatin interaction
ENSG00000158092	Chromatin interaction
ENSG00000240695	Chromatin interaction
ENSG00000239213	Chromatin interaction
ENSG00000158169	Chromatin interaction
ENSG00000196542	Chromatin interaction
ENSG00000168917	Chromatin interaction
ENSG00000251708	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1048145	0.82[EUR][1000 genomes]
rs10513016	0.82[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs16844056	0.87[EUR][1000 genomes]
rs17301365	0.82[EUR][1000 genomes]
rs17365351	0.82[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs17466223	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs55763637	0.83[EUR][1000 genomes]
rs56308712	0.90[EUR][1000 genomes]
rs56888009	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57466072	0.89[EUR][1000 genomes]
rs57681357	0.83[EUR][1000 genomes]
rs59361983	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59616231	0.82[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs59696368	0.82[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs66470158	0.82[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs66471262	0.82[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs66637228	0.89[EUR][1000 genomes]
rs66739346	0.89[EUR][1000 genomes]
rs66902780	0.84[EUR][1000 genomes]
rs67231188	0.89[EUR][1000 genomes]
rs67236827	0.82[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs67888773	0.82[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs67923745	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68018658	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6805814	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72975363	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73228025	0.82[EUR][1000 genomes]
rs73228037	0.84[EUR][1000 genomes]
rs73228040	0.84[EUR][1000 genomes]
rs73230052	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73230065	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73230077	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73230078	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73230095	0.93[EUR][1000 genomes]
rs73231917	0.90[EUR][1000 genomes]
rs73231937	0.87[EUR][1000 genomes]
rs73231953	0.82[EUR][1000 genomes]
rs73231958	0.81[EUR][1000 genomes]
rs73231966	0.82[EUR][1000 genomes]
rs73231974	0.82[EUR][1000 genomes]
rs73231975	0.82[EUR][1000 genomes]
rs7646563	0.89[EUR][1000 genomes]
rs7646723	0.89[EUR][1000 genomes]
rs923001	0.82[AFR][1000 genomes];0.90[EUR][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	nsv877529	chr3:136364511-136487559	ZNF genes & repeats Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv1006737	chr3:136466188-136530743	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
3	esv3423516	chr3:136469287-136472135	Flanking Active TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs67546863	IL20RB	cis	Nerve Tibial	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:136468200-136473000	Active TSS	A549	lung
2	chr3:136468400-136472000	Active TSS	NHDF-Ad	bronchial
3	chr3:136468400-136472200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr3:136468400-136472200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr3:136468400-136472600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr3:136468600-136472200	Active TSS	Breast Myoepithelial Primary Cells	Breast
7	chr3:136468800-136472000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr3:136468800-136472000	Active TSS	HMEC	breast
9	chr3:136468800-136472200	Active TSS	GM12878-XiMat	blood
10	chr3:136469000-136472000	Active TSS	Fetal Kidney	kidney
11	chr3:136469000-136472000	Active TSS	Hela-S3	cervix
12	chr3:136469000-136472200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr3:136469000-136472400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr3:136469000-136472400	Active TSS	Fetal Muscle Trunk	muscle
15	chr3:136469000-136472600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr3:136469000-136472600	Active TSS	Colonic Mucosa	Colon
17	chr3:136469200-136472000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr3:136469200-136472000	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
19	chr3:136469200-136472000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr3:136469200-136472000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
21	chr3:136469200-136472000	Active TSS	Fetal Intestine Small	intestine
22	chr3:136469200-136472000	Active TSS	Placenta Amnion	Placenta Amnion
23	chr3:136469200-136472000	Active TSS	NHLF	lung
24	chr3:136469200-136472200	Active TSS	Brain Anterior Caudate	brain
25	chr3:136469200-136472200	Active TSS	Fetal Intestine Large	intestine
26	chr3:136469200-136472200	Active TSS	Stomach Smooth Muscle	stomach
27	chr3:136469200-136472400	Active TSS	Aorta	Aorta
28	chr3:136469200-136472400	Active TSS	Left Ventricle	heart
29	chr3:136469200-136472400	Active TSS	Ovary	ovary
30	chr3:136469200-136472400	Active TSS	Psoas Muscle	Psoas
31	chr3:136469200-136472400	Active TSS	Right Ventricle	heart
32	chr3:136469200-136473000	Active TSS	H9 Cell Line	embryonic stem cell
33	chr3:136469200-136473400	Active TSS	K562	blood
34	chr3:136469400-136472000	Active TSS	Cortex derived primary cultured neurospheres	brain
35	chr3:136469400-136472000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr3:136469400-136472000	Active TSS	Fetal Brain Female	brain
37	chr3:136469400-136472000	Active TSS	Fetal Muscle Leg	muscle
38	chr3:136469400-136472000	Active TSS	Fetal Thymus	thymus
39	chr3:136469400-136472000	Active TSS	NHEK	skin
40	chr3:136469400-136472200	Active TSS	H1 Cell Line	embryonic stem cell
41	chr3:136469400-136472200	Active TSS	HUES6 Cell Line	embryonic stem cell
42	chr3:136469400-136472200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
43	chr3:136469400-136472200	Active TSS	Liver	Liver
44	chr3:136469400-136472200	Active TSS	Fetal Stomach	stomach
45	chr3:136469400-136472200	Active TSS	HSMM	muscle
46	chr3:136469400-136472400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr3:136469400-136472400	Active TSS	Brain Germinal Matrix	brain
48	chr3:136469400-136472600	Active TSS	ES-I3 Cell Line	embryonic stem cell
49	chr3:136469400-136472600	Active TSS	HSMMtube	muscle
50	chr3:136469600-136472000	Active TSS	iPS-20b Cell Line	embryonic stem cell

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