Variant report

Variant	rs3764084
Chromosome Location	chr13:50071062-50071063
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr13:50069393-50071679	GM12878	blood:	n/a	n/a
2	POLR2A	chr13:50069269-50072180	GM12878	blood:	n/a	n/a
3	POLR2A	chr13:50070266-50072102	GM12878	blood:	n/a	n/a
4	POLR2A	chr13:50069336-50071342	GM12892	blood:	n/a	n/a
5	POLR2A	chr13:50069358-50071354	GM19193	blood:	n/a	n/a
6	POLR2A	chr13:50071001-50071328	HepG2	liver:	n/a	n/a
7	POLR2A	chr13:50069392-50072153	GM12891	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr13:50016481..50018378-chr13:50070335..50072171,3	K562	blood:
2	chr13:50016483..50020444-chr13:50068529..50072853,4	MCF-7	breast:
3	chr13:50016715..50020360-chr13:50068508..50074036,7	MCF-7	breast:
4	chr13:50061049..50067624-chr13:50068104..50073631,8	MCF-7	breast:
5	chr13:50068906..50071236-chr13:50159028..50161203,3	MCF-7	breast:
6	chr13:50061212..50063170-chr13:50068743..50071652,2	MCF-7	breast:

No data

Variant related genes	Relation type
PHF11	TF binding region
ENSG00000236577	Chromatin interaction
ENSG00000136169	Chromatin interaction
ENSG00000102547	Chromatin interaction
ENSG00000136144	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11619265	0.81[EUR][1000 genomes]
rs12429813	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1409017	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2057414	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2057416	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35980977	0.81[EUR][1000 genomes]
rs3764089	0.82[EUR][1000 genomes]
rs3765526	0.80[AFR][1000 genomes]
rs4340215	0.82[AFR][1000 genomes]
rs4430650	0.82[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs4941643	0.84[EUR][1000 genomes]
rs4942833	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6561526	0.84[EUR][1000 genomes]
rs7326345	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7997737	0.81[ASN][1000 genomes]
rs9316454	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9526565	0.80[AFR][1000 genomes]
rs9526567	0.81[AFR][1000 genomes]
rs9526568	0.81[AFR][1000 genomes]
rs9535251	0.81[ASN][1000 genomes]
rs9805560	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1047311	chr13:49895019-50224227	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv430561	chr13:49930643-50089844	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv430566	chr13:49945247-50089844	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv430570	chr13:49961137-50089844	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv523648	chr13:50005444-50086266	Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv561613	chr13:50013622-50086266	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv900070	chr13:50013622-50087142	Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	nsv561614	chr13:50042983-50086253	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv561615	chr13:50042983-50086266	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	nsv916093	chr13:50050919-50290245	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3764084	CAB39L	Cis_1M	lymphoblastoid	RTeQTL
rs3764084	PHF11	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50069000-50071400	Active TSS	HUES6 Cell Line	embryonic stem cell
2	chr13:50069000-50071400	Active TSS	Stomach Smooth Muscle	stomach
3	chr13:50069000-50071800	Active TSS	Duodenum Smooth Muscle	Duodenum
4	chr13:50069200-50071200	Active TSS	Primary T helper cells PMA-I stimulated	--
5	chr13:50069200-50071200	Active TSS	Thymus	Thymus
6	chr13:50069200-50071200	Active TSS	GM12878-XiMat	blood
7	chr13:50069200-50071800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr13:50070200-50089200	Weak transcription	Fetal Brain Male	brain
9	chr13:50070400-50071200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
10	chr13:50070400-50071200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr13:50070400-50071200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr13:50070400-50071200	Flanking Active TSS	Dnd41	blood
13	chr13:50070400-50072200	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
14	chr13:50070600-50073400	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr13:50070800-50071200	Active TSS	Duodenum Mucosa	Duodenum
16	chr13:50070800-50071200	Flanking Active TSS	Fetal Thymus	thymus
17	chr13:50070800-50071400	Weak transcription	Lung	lung
18	chr13:50070800-50071400	Active TSS	Skeletal Muscle Male	skeletal muscle
19	chr13:50070800-50071600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr13:50070800-50071600	Enhancers	K562	blood
21	chr13:50070800-50072600	Weak transcription	Liver	Liver
22	chr13:50070800-50072800	Weak transcription	Fetal Intestine Large	intestine
23	chr13:50070800-50073600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr13:50070800-50073600	Weak transcription	HMEC	breast
25	chr13:50070800-50074200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr13:50070800-50074400	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr13:50070800-50074400	Weak transcription	Small Intestine	intestine
28	chr13:50070800-50074800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
29	chr13:50070800-50076200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr13:50070800-50076200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr13:50070800-50076400	Weak transcription	Fetal Lung	lung
32	chr13:50070800-50076800	Weak transcription	Left Ventricle	heart
33	chr13:50070800-50077000	Weak transcription	Gastric	stomach
34	chr13:50070800-50086600	Weak transcription	Psoas Muscle	Psoas
35	chr13:50070800-50086800	Weak transcription	Ovary	ovary
36	chr13:50070800-50087400	Weak transcription	Placenta	Placenta
37	chr13:50070800-50087600	Weak transcription	Fetal Muscle Trunk	muscle
38	chr13:50070800-50087800	Weak transcription	Aorta	Aorta
39	chr13:50070800-50087800	Weak transcription	NHEK	skin
40	chr13:50070800-50088000	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr13:50070800-50088000	Weak transcription	Brain Anterior Caudate	brain
42	chr13:50070800-50088000	Weak transcription	Esophagus	oesophagus
43	chr13:50070800-50088000	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr13:50070800-50088200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr13:50070800-50088200	Weak transcription	Brain Substantia Nigra	brain
46	chr13:50070800-50095600	Weak transcription	Fetal Kidney	kidney
47	chr13:50071000-50071200	Enhancers	Primary B cells from cord blood	blood
48	chr13:50071000-50071400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr13:50071000-50071400	Weak transcription	Primary hematopoietic stem cells	blood
50	chr13:50071000-50071400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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