Variant report

Variant	rs3794533
Chromosome Location	chr15:52074573-52074574
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:36)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:36 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr15:52074570-52074938	A549	lung:	n/a	n/a
2	RAD21	chr15:52074446-52075099	HCT-116	colon:	n/a	n/a
3	RAD21	chr15:52074569-52074925	IMR90	lung:	n/a	n/a
4	RAD21	chr15:52074518-52075006	ECC-1	luminal epithelium:	n/a	n/a
5	CBX3	chr15:52074501-52075007	HCT-116	colon:	n/a	n/a
6	RAD21	chr15:52074567-52074926	HepG2	liver:	n/a	n/a
7	RAD21	chr15:52074521-52074987	ECC-1	luminal epithelium:	n/a	n/a
8	RAD21	chr15:52074462-52074948	MCF-7	breast:	n/a	n/a
9	CBX3	chr15:52074527-52075001	K562	blood:	n/a	n/a
10	CTCF	chr15:52074519-52074960	K562	blood:	n/a	n/a
11	RAD21	chr15:52074522-52075145	SK-N-SH	brain:	n/a	n/a
12	SMC3	chr15:52074554-52075018	Hela-S3	cervix:	n/a	n/a
13	KAP1	chr15:52074513-52074959	K562	blood:	n/a	n/a
14	RAD21	chr15:52074459-52075086	A549	lung:	n/a	n/a
15	RAD21	chr15:52074505-52075040	HCT-116	colon:	n/a	n/a
16	RAD21	chr15:52074560-52074924	A549	lung:	n/a	n/a
17	CTCF	chr15:52074384-52075061	HCT-116	colon:	n/a	n/a
18	CTCF	chr15:52074560-52074710	GM06990	blood:	n/a	n/a
19	RAD21	chr15:52074555-52074991	Hela-S3	cervix:	n/a	n/a
20	CTCF	chr15:52074366-52075071	SK-N-SH	brain:	n/a	n/a
21	CTCF	chr15:52073992-52075147	A549	lung:	n/a	n/a
22	CTCF	chr15:52074524-52074909	H1-hESC	embryonic stem cell:	n/a	n/a
23	CTCF	chr15:52074528-52074959	K562	blood:	n/a	n/a
24	RAD21	chr15:52074543-52074977	HepG2	liver:	n/a	n/a
25	CTCF	chr15:52074560-52074710	NHEK	skin:	n/a	n/a
26	CTCF	chr15:52074461-52074941	MCF-7	breast:	n/a	n/a
27	RAD21	chr15:52074437-52075012	MCF-7	breast:	n/a	n/a
28	RAD21	chr15:52074531-52074984	H1-hESC	embryonic stem cell:	n/a	n/a
29	CTCF	chr15:52074546-52074931	HepG2	liver:	n/a	n/a
30	RAD21	chr15:52074406-52075097	A549	lung:	n/a	n/a
31	STAT3	chr15:52074509-52075058	MCF10A-Er-Src	breast:	n/a	chr15:52075033-52075047
32	RAD21	chr15:52074457-52074993	H1-hESC	embryonic stem cell:	n/a	n/a
33	CTCF	chr15:52074451-52075108	MCF-7	breast:	n/a	n/a
34	RAD21	chr15:52074452-52074998	H1-hESC	embryonic stem cell:	n/a	n/a
35	RAD21	chr15:52074564-52074936	HepG2	liver:	n/a	n/a
36	SRF	chr15:52074505-52075012	HCT-116	colon:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:52072694..52074758-chr15:52121019..52123367,2	MCF-7	breast:
2	chr15:52074262..52074783-chr15:52431783..52432627,2	MCF-7	breast:
3	chr15:52071204..52073372-chr15:52073391..52075990,2	MCF-7	breast:
4	chr15:52072134..52075031-chr15:52213597..52215274,2	MCF-7	breast:
5	chr15:52041956..52043686-chr15:52074164..52076601,2	MCF-7	breast:
6	chr15:52072025..52074741-chr15:52120265..52123225,4	MCF-7	breast:
7	chr15:52073675..52076293-chr15:52262420..52265302,2	MCF-7	breast:

No data

Variant related genes	Relation type
TMOD2	TF binding region
ENSG00000069966	Chromatin interaction
ENSG00000128872	Chromatin interaction
ENSG00000166477	Chromatin interaction
ENSG00000138594	Chromatin interaction
ENSG00000140280	Chromatin interaction

Extended variants
information (count: 121 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:119)

rs_ID	r²[population]
rs1025185	1.00[EUR][1000 genomes]
rs10519323	1.00[CHB][hapmap];0.86[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10519325	1.00[EUR][1000 genomes]
rs10519326	1.00[EUR][1000 genomes]
rs12438469	1.00[EUR][1000 genomes]
rs12442283	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1378891	1.00[EUR][1000 genomes]
rs1426085	1.00[EUR][1000 genomes]
rs1426086	1.00[EUR][1000 genomes]
rs16964486	1.00[YRI][hapmap]
rs16964523	0.86[JPT][hapmap];0.92[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs17649047	1.00[CHB][hapmap];0.86[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17649178	1.00[CHB][hapmap];0.86[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17649208	0.86[JPT][hapmap]
rs17649255	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17649391	1.00[EUR][1000 genomes]
rs17649692	1.00[EUR][1000 genomes]
rs17649801	1.00[EUR][1000 genomes]
rs17705373	1.00[YRI][hapmap]
rs17705530	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17705649	1.00[CHB][hapmap];0.86[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17705685	0.86[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17705889	1.00[EUR][1000 genomes]
rs17706076	1.00[EUR][1000 genomes]
rs2052707	1.00[EUR][1000 genomes]
rs2162224	1.00[EUR][1000 genomes]
rs2414118	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2436664	1.00[EUR][1000 genomes]
rs2470613	1.00[EUR][1000 genomes]
rs2554309	1.00[EUR][1000 genomes]
rs2554310	1.00[EUR][1000 genomes]
rs2554311	1.00[EUR][1000 genomes]
rs2554318	1.00[EUR][1000 genomes]
rs2554323	1.00[EUR][1000 genomes]
rs2554325	1.00[EUR][1000 genomes]
rs2554326	1.00[EUR][1000 genomes]
rs2554330	1.00[EUR][1000 genomes]
rs2554333	1.00[EUR][1000 genomes]
rs2554351	1.00[EUR][1000 genomes]
rs2554352	1.00[EUR][1000 genomes]
rs2554356	1.00[EUR][1000 genomes]
rs2570218	1.00[EUR][1000 genomes]
rs2570219	1.00[EUR][1000 genomes]
rs2570220	1.00[EUR][1000 genomes]
rs2570221	1.00[EUR][1000 genomes]
rs2570227	1.00[EUR][1000 genomes]
rs2570242	1.00[EUR][1000 genomes]
rs2570244	1.00[EUR][1000 genomes]
rs2570245	1.00[EUR][1000 genomes]
rs2570247	1.00[EUR][1000 genomes]
rs2570249	1.00[EUR][1000 genomes]
rs2570250	1.00[EUR][1000 genomes]
rs2570256	1.00[EUR][1000 genomes]
rs2570257	1.00[EUR][1000 genomes]
rs2570259	1.00[EUR][1000 genomes]
rs2570261	1.00[EUR][1000 genomes]
rs2570267	1.00[EUR][1000 genomes]
rs2570270	1.00[EUR][1000 genomes]
rs2570273	1.00[EUR][1000 genomes]
rs2570274	1.00[EUR][1000 genomes]
rs2593165	1.00[EUR][1000 genomes]
rs2593175	1.00[EUR][1000 genomes]
rs2593176	1.00[EUR][1000 genomes]
rs2593180	1.00[EUR][1000 genomes]
rs2623246	1.00[EUR][1000 genomes]
rs2623250	1.00[EUR][1000 genomes]
rs2623252	1.00[EUR][1000 genomes]
rs2623257	1.00[EUR][1000 genomes]
rs2623260	1.00[EUR][1000 genomes]
rs2623264	1.00[EUR][1000 genomes]
rs2623267	1.00[EUR][1000 genomes]
rs2623268	1.00[EUR][1000 genomes]
rs2623269	1.00[EUR][1000 genomes]
rs2623277	1.00[EUR][1000 genomes]
rs2623278	1.00[EUR][1000 genomes]
rs2623287	1.00[EUR][1000 genomes]
rs2899483	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2916174	1.00[EUR][1000 genomes]
rs2959297	1.00[EUR][1000 genomes]
rs2959303	1.00[EUR][1000 genomes]
rs3099570	1.00[EUR][1000 genomes]
rs34407523	1.00[EUR][1000 genomes]
rs36097346	0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3751595	1.00[YRI][hapmap]
rs3794537	1.00[CHB][hapmap];0.86[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4774600	1.00[EUR][1000 genomes]
rs4774601	1.00[CHB][hapmap];0.86[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4775971	0.89[AMR][1000 genomes]
rs4775979	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4775987	1.00[EUR][1000 genomes]
rs4775988	1.00[EUR][1000 genomes]
rs4775989	1.00[EUR][1000 genomes]
rs56221158	0.82[AMR][1000 genomes]
rs7165594	1.00[YRI][hapmap]
rs7166322	1.00[CHB][hapmap];0.86[JPT][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7166954	0.86[AMR][1000 genomes]
rs7167759	1.00[YRI][hapmap]
rs7168775	1.00[YRI][hapmap]
rs7170429	1.00[CHB][hapmap];0.86[JPT][hapmap];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7170700	0.86[JPT][hapmap];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7173661	1.00[CHB][hapmap];0.86[JPT][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7179139	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7179971	0.82[AMR][1000 genomes]
rs7180093	0.82[AMR][1000 genomes]
rs72730966	0.89[ASN][1000 genomes]
rs73407386	0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73407396	0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73409011	0.92[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs73411105	1.00[EUR][1000 genomes]
rs74015757	0.87[AMR][1000 genomes]
rs74015761	0.84[AMR][1000 genomes]
rs8024441	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8026507	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8027426	1.00[CHB][hapmap];0.86[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8034090	1.00[YRI][hapmap]
rs8038895	1.00[YRI][hapmap]
rs8042310	1.00[EUR][1000 genomes]
rs919057	1.00[EUR][1000 genomes]
rs990666	1.00[EUR][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	nsv569409	chr15:52028914-52268144	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	esv3411789	chr15:52052789-52087519	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52051200-52077600	Weak transcription	Psoas Muscle	Psoas
2	chr15:52052200-52074600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr15:52052200-52076000	Weak transcription	Fetal Brain Male	brain
4	chr15:52052200-52101800	Weak transcription	Colonic Mucosa	Colon
5	chr15:52052400-52078400	Weak transcription	Rectal Smooth Muscle	rectum
6	chr15:52052600-52106600	Weak transcription	HSMM	muscle
7	chr15:52053400-52090600	Weak transcription	Pancreas	Pancrea
8	chr15:52060200-52103400	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr15:52060400-52079200	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr15:52060400-52085400	Weak transcription	Fetal Lung	lung
11	chr15:52060600-52087400	Weak transcription	Gastric	stomach
12	chr15:52060600-52088400	Weak transcription	Duodenum Mucosa	Duodenum
13	chr15:52060600-52091000	Weak transcription	Right Ventricle	heart
14	chr15:52060800-52074600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr15:52060800-52101200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr15:52060800-52102600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr15:52060800-52105400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr15:52061600-52085400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr15:52061600-52112000	Weak transcription	NHLF	lung
20	chr15:52061800-52076200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr15:52061800-52077200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr15:52061800-52098600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr15:52063000-52074600	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr15:52064400-52090400	Weak transcription	Left Ventricle	heart
25	chr15:52064600-52078400	Weak transcription	Fetal Muscle Leg	muscle
26	chr15:52065600-52090600	Weak transcription	Spleen	Spleen
27	chr15:52065800-52091000	Weak transcription	Esophagus	oesophagus
28	chr15:52067200-52090600	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr15:52067400-52074600	Weak transcription	Dnd41	blood
30	chr15:52067400-52078400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr15:52067400-52079800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr15:52067600-52090600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr15:52067800-52074600	Weak transcription	Fetal Muscle Trunk	muscle
34	chr15:52067800-52089000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr15:52068400-52078200	Weak transcription	Thymus	Thymus
36	chr15:52068400-52079200	Weak transcription	Fetal Stomach	stomach
37	chr15:52069200-52074600	Weak transcription	Adipose Nuclei	Adipose
38	chr15:52069200-52074600	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr15:52069200-52078400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr15:52069200-52091000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr15:52069400-52074800	Weak transcription	Colon Smooth Muscle	Colon
42	chr15:52069400-52074800	Weak transcription	Fetal Intestine Small	intestine
43	chr15:52069400-52075800	Weak transcription	Fetal Intestine Large	intestine
44	chr15:52069400-52076800	Weak transcription	Liver	Liver
45	chr15:52069400-52078800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
46	chr15:52069400-52085200	Weak transcription	Pancreatic Islets	Pancreatic Islet
47	chr15:52070000-52074800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr15:52071000-52080400	Strong transcription	Monocytes-CD14+_RO01746	blood
49	chr15:52071200-52077600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
50	chr15:52071200-52079000	Weak transcription	H9 Cell Line	embryonic stem cell

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