Variant report

Variant	rs2804633
Chromosome Location	chr10:38691130-38691131
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	POLR2A	chr10:38690756-38693454	GM12892	blood:	n/a	n/a
2	POLR2A	chr10:38691074-38691224	HepG2	liver:	n/a	n/a
3	SIN3AK20	chr10:38691056-38691195	HepG2	liver:	n/a	n/a
4	MYBL2	chr10:38691044-38692400	HepG2	liver:	n/a	n/a
5	POLR2A	chr10:38690522-38693601	GM12892	blood:	n/a	n/a
6	FOXA1	chr10:38690625-38691141	HepG2	liver:	n/a	n/a
7	TCF12	chr10:38691027-38691247	GM12878	blood:	n/a	n/a
8	POU2F2	chr10:38690863-38693502	GM12878	blood:	n/a	n/a
9	HA-E2F1	chr10:38690720-38692486	MCF-7	breast:	n/a	n/a
10	HEY1	chr10:38691108-38693448	K562	blood:	n/a	n/a
11	RCOR1	chr10:38691096-38691977	IMR90	lung:	n/a	n/a
12	TAF1	chr10:38691127-38691882	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr10:38691103-38692414	GM19193	blood:	n/a	n/a
14	HEY1	chr10:38690450-38693063	HepG2	liver:	n/a	n/a
15	MXI1	chr10:38691075-38692514	SK-N-SH	brain:	n/a	n/a
16	POLR2A	chr10:38689909-38693482	GM12892	blood:	n/a	n/a
17	POLR2A	chr10:38689987-38693615	GM12878	blood:	n/a	n/a
18	POLR2A	chr10:38690697-38693726	H1-hESC	embryonic stem cell:	n/a	n/a
19	POLR2A	chr10:38690535-38693500	GM12878	blood:	n/a	n/a
20	PAX5	chr10:38690761-38692710	GM12878	blood:	n/a	n/a
21	POLR2A	chr10:38690739-38691149	Hela-S3	cervix:	n/a	n/a

Variant related genes	Relation type
SEPT7P9	TF binding region

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs17595369	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17595376	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17595494	0.80[ASN][1000 genomes]
rs2754358	0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2754362	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2754369	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2754373	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2754381	0.86[ASN][1000 genomes]
rs2800475	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2800483	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2800542	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2804634	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2804645	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2804676	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4006909	0.84[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs9340228	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9731098	0.82[ASN][1000 genomes]
rs9731321	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv427860	chr10:38588021-38818835	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv895034	chr10:38632352-38743545	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	esv2764202	chr10:38641508-39076221	Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv1048953	chr10:38645824-39074038	Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv428230	chr10:38652001-38818835	ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	esv2757379	chr10:38677023-38978680	Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	esv2759744	chr10:38677023-39154935	ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
8	nsv947860	chr10:38678275-38747483	Active TSS Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Genic enhancers	TF binding region CpG island lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv895035	chr10:38678941-38739427	Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Bivalent/Poised TSS	TF binding region CpG island lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv895036	chr10:38678941-38741100	Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv895037	chr10:38678941-38741777	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island lncRNA	5 gene(s)	inside rSNPs	diseases
12	nsv895038	chr10:38678941-38890240	ZNF genes & repeats Active TSS Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
13	nsv1036840	chr10:38682579-39074038	ZNF genes & repeats Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
14	nsv948258	chr10:38683949-38693538	Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Enhancers ZNF genes & repeats	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases
15	nsv540569	chr10:38689167-38769822	Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent/Poised TSS	TF binding region CpG island lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:38690000-38692600	Active TSS	HepG2	liver
2	chr10:38690400-38692600	Active TSS	Duodenum Mucosa	Duodenum
3	chr10:38690400-38692600	Active TSS	Pancreatic Islets	Pancreatic Islet
4	chr10:38690400-38692600	Active TSS	Pancreas	Pancrea
5	chr10:38690400-38692600	Active TSS	Rectal Mucosa Donor 31	rectum
6	chr10:38690400-38692800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr10:38690400-38692800	Active TSS	Primary hematopoietic stem cells short term culture	blood
8	chr10:38690400-38692800	Active TSS	Fetal Intestine Small	intestine
9	chr10:38690400-38692800	Active TSS	GM12878-XiMat	blood
10	chr10:38690400-38693000	Active TSS	Liver	Liver
11	chr10:38690600-38691200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr10:38690600-38691200	Weak transcription	Brain Substantia Nigra	brain
13	chr10:38690600-38691600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr10:38690600-38692600	Active TSS	Fetal Intestine Large	intestine
15	chr10:38690600-38692600	Active TSS	Rectal Smooth Muscle	rectum
16	chr10:38690600-38692800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr10:38690600-38692800	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
18	chr10:38690600-38692800	Active TSS	Brain Anterior Caudate	brain
19	chr10:38690600-38692800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
20	chr10:38690600-38693000	Active TSS	Colonic Mucosa	Colon
21	chr10:38690600-38693000	Active TSS	HSMM	muscle
22	chr10:38690800-38691200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
23	chr10:38690800-38692200	Active TSS	Primary T helper cells PMA-I stimulated	--
24	chr10:38690800-38692600	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr10:38690800-38692600	Active TSS	NHLF	lung
26	chr10:38690800-38692800	Active TSS	iPS-18 Cell Line	embryonic stem cell
27	chr10:38690800-38692800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr10:38690800-38692800	Active TSS	Brain Inferior Temporal Lobe	brain
29	chr10:38690800-38692800	Active TSS	Rectal Mucosa Donor 29	rectum
30	chr10:38690800-38693000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr10:38690800-38693000	Active TSS	Right Ventricle	heart
32	chr10:38690800-38693000	Active TSS	A549	lung
33	chr10:38690800-38693000	Active TSS	K562	blood
34	chr10:38691000-38691200	Active TSS	Primary B cells from cord blood	blood
35	chr10:38691000-38691200	Active TSS	Primary T helper cells fromperipheralblood	blood
36	chr10:38691000-38691200	Flanking Active TSS	Placenta	Placenta
37	chr10:38691000-38691200	Active TSS	HMEC	breast
38	chr10:38691000-38691400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
39	chr10:38691000-38691400	Flanking Active TSS	Primary B cells from peripheral blood	blood
40	chr10:38691000-38691400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
41	chr10:38691000-38691400	Flanking Active TSS	Primary hematopoietic stem cells	blood
42	chr10:38691000-38691400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
43	chr10:38691000-38691400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr10:38691000-38691400	Enhancers	Fetal Brain Male	brain
45	chr10:38691000-38691400	Flanking Active TSS	Fetal Muscle Leg	muscle
46	chr10:38691000-38691400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
47	chr10:38691000-38691400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
48	chr10:38691000-38691600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr10:38691000-38691600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
50	chr10:38691000-38691600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood

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