Variant report

Variant	rs2230592
Chromosome Location	chr3:49936608-49936609
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:45)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:45 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr3:49936551-49936759	HepG2	liver:	n/a	n/a
2	CTCF	chr3:49936480-49936630	HAc	cerebellar:	n/a	n/a
3	CTCF	chr3:49936560-49936710	K562	blood:	n/a	n/a
4	CTCF	chr3:49936560-49936710	HPAF	blood vessel:	n/a	n/a
5	CTCF	chr3:49936539-49936739	K562	blood:	n/a	n/a
6	CTCF	chr3:49936528-49936717	MCF-7	breast:	n/a	n/a
7	CTCF	chr3:49936480-49936630	HRPEpiC	eye:	n/a	n/a
8	CTCF	chr3:49936538-49936813	K562	blood:	n/a	n/a
9	RAD21	chr3:49936586-49936669	H1-hESC	embryonic stem cell:	n/a	n/a
10	CTCF	chr3:49936560-49936710	Hela-S3	cervix:	n/a	n/a
11	CTCF	chr3:49936560-49936710	SK-N-SH_RA	brain:	n/a	n/a
12	SMC3	chr3:49936605-49936689	HepG2	liver:	n/a	n/a
13	CTCF	chr3:49936560-49936710	HEK293	kidney:	n/a	n/a
14	CTCF	chr3:49936576-49936699	Hela-S3	cervix:	n/a	n/a
15	CTCF	chr3:49936560-49936710	HepG2	liver:	n/a	n/a
16	CTCF	chr3:49936560-49936710	WERI-Rb-1	eye:	n/a	n/a
17	POLR2A	chr3:49936289-49936981	MCF-7	breast:	n/a	n/a
18	CTCF	chr3:49936600-49936750	HEEpiC	esophagus:	n/a	n/a
19	CTCF	chr3:49936584-49936731	K562	blood:	n/a	n/a
20	CTCF	chr3:49936560-49936710	A549	lung:	n/a	n/a
21	CTCF	chr3:49936600-49936750	HCT-116	colon:	n/a	n/a
22	CTCF	chr3:49936600-49936750	SAEC	small airway:	n/a	n/a
23	BHLHE40	chr3:49936509-49936775	HepG2	liver:	n/a	n/a
24	CTCF	chr3:49936584-49936711	H1-hESC	embryonic stem cell:	n/a	n/a
25	CTCF	chr3:49936576-49936706	MCF-7	breast:	n/a	n/a
26	CTCF	chr3:49936520-49936670	WERI-Rb-1	eye:	n/a	n/a
27	CTCF	chr3:49936500-49936650	HCFaa	heart:	n/a	n/a
28	CTCF	chr3:49936569-49936673	MCF-7	breast:	n/a	n/a
29	CTCF	chr3:49936580-49936730	HMEC	breast:	n/a	n/a
30	RAD21	chr3:49936599-49936666	HepG2	liver:	n/a	n/a
31	CTCF	chr3:49936560-49936710	AG04449	skin:	n/a	n/a
32	MYC	chr3:49936543-49936635	MCF-7	breast:	n/a	n/a
33	CTCF	chr3:49936570-49936714	HepG2	liver:	n/a	n/a
34	CTCF	chr3:49936496-49936708	NHEK	skin:	n/a	n/a
35	CTCF	chr3:49936480-49936630	GM12864	blood:	n/a	n/a
36	ZKSCAN1	chr3:49936501-49936751	Hela-S3	cervix:	n/a	n/a
37	CTCF	chr3:49936460-49936610	SAEC	small airway:	n/a	n/a
38	CTCF	chr3:49936560-49936710	HBMEC	blood vessel:	n/a	n/a
39	CTCF	chr3:49936500-49936650	Hela-S3	cervix:	n/a	n/a
40	CTCF	chr3:49936582-49936701	MCF-7	breast:	n/a	n/a
41	CTCF	chr3:49936560-49936710	HMF	breast:	n/a	n/a
42	RAD21	chr3:49936490-49936767	HepG2	liver:	n/a	n/a
43	CTCF	chr3:49936533-49936736	MCF-7	breast:	n/a	n/a
44	CTCF	chr3:49936500-49936650	HCPEpiC	choroid plexus:	n/a	n/a
45	CTCF	chr3:49936607-49936668	K562	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:49935827..49937610-chr3:49975872..49978554,2	K562	blood:
2	chr3:49933351..49938041-chr3:49938966..49942332,9	K562	blood:
3	chr3:49839049..49842350-chr3:49936029..49940414,4	K562	blood:
4	chr3:49927426..49930206-chr3:49934919..49938158,3	K562	blood:
5	chr3:49840382..49843169-chr3:49936309..49938239,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000228008	TF binding region
ENSG00000230698	TF binding region
MST1R	TF binding region
ENSG00000228008	Chromatin interaction
ENSG00000164078	Chromatin interaction
ENSG00000185614	Chromatin interaction
ENSG00000004534	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs17050918	1.00[YRI][hapmap]
rs28424211	0.89[AFR][1000 genomes]
rs35340753	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56057035	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56352827	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57347154	0.89[AFR][1000 genomes]
rs61156427	0.89[AFR][1000 genomes]
rs73831918	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73832783	0.89[AFR][1000 genomes]
rs73834119	0.89[AFR][1000 genomes]
rs73834125	0.89[AFR][1000 genomes]
rs73834127	0.89[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1796352	chr3:49687101-49949959	Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
2	nsv834688	chr3:49811115-50019299	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	nsv876766	chr3:49817450-49961780	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	nsv876767	chr3:49918751-50153356	Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49919600-49937800	Weak transcription	Small Intestine	intestine
2	chr3:49920000-49943000	Weak transcription	Brain Anterior Caudate	brain
3	chr3:49920200-49938400	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr3:49920400-49938200	Weak transcription	Left Ventricle	heart
5	chr3:49920600-49938200	Weak transcription	Fetal Muscle Leg	muscle
6	chr3:49920600-49938200	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr3:49924000-49937600	Strong transcription	Fetal Stomach	stomach
8	chr3:49924600-49937600	Weak transcription	K562	blood
9	chr3:49924800-49938200	Weak transcription	Right Ventricle	heart
10	chr3:49925200-49941200	Weak transcription	Brain Germinal Matrix	brain
11	chr3:49926600-49938400	Weak transcription	Aorta	Aorta
12	chr3:49927000-49938000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr3:49927400-49936800	Weak transcription	Fetal Thymus	thymus
14	chr3:49927400-49937600	Weak transcription	Placenta	Placenta
15	chr3:49927600-49940400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr3:49928600-49943000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr3:49929000-49938400	Weak transcription	Fetal Muscle Trunk	muscle
18	chr3:49929600-49941200	Weak transcription	Ovary	ovary
19	chr3:49931400-49938400	Weak transcription	Colon Smooth Muscle	Colon
20	chr3:49931400-49943600	Weak transcription	Brain Hippocampus Middle	brain
21	chr3:49933200-49938200	Weak transcription	Adipose Nuclei	Adipose
22	chr3:49933400-49939600	Weak transcription	Fetal Brain Female	brain
23	chr3:49933800-49941400	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr3:49934200-49938600	Weak transcription	Fetal Lung	lung
25	chr3:49934400-49941400	Weak transcription	Brain Angular Gyrus	brain
26	chr3:49934800-49936800	Weak transcription	A549	lung
27	chr3:49935200-49937600	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr3:49935400-49937200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr3:49935400-49937400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr3:49935400-49937800	Weak transcription	Stomach Smooth Muscle	stomach
31	chr3:49935400-49940000	Weak transcription	Spleen	Spleen
32	chr3:49935600-49937400	Weak transcription	HepG2	liver
33	chr3:49935800-49937600	Weak transcription	Rectal Smooth Muscle	rectum
34	chr3:49936000-49936800	Strong transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr3:49936000-49936800	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
36	chr3:49936000-49937600	Enhancers	HMEC	breast
37	chr3:49936000-49939000	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr3:49936200-49936800	Enhancers	Esophagus	oesophagus
39	chr3:49936200-49936800	Transcr. at gene 5' and 3'	Hela-S3	cervix
40	chr3:49936200-49937000	Genic enhancers	Colonic Mucosa	Colon
41	chr3:49936200-49938800	Transcr. at gene 5' and 3'	NHEK	skin
42	chr3:49936200-49939000	Enhancers	Lung	lung
43	chr3:49936200-49941000	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr3:49936400-49936800	Weak transcription	Fetal Intestine Large	intestine
45	chr3:49936400-49937000	Genic enhancers	Sigmoid Colon	Sigmoid Colon
46	chr3:49936400-49937200	Genic enhancers	Duodenum Mucosa	Duodenum
47	chr3:49936400-49937600	Genic enhancers	Fetal Intestine Small	intestine
48	chr3:49936400-49940800	Enhancers	Pancreas	Pancrea
49	chr3:49936600-49936800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr3:49936600-49936800	Flanking Active TSS	Stomach Mucosa	stomach

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