Variant report

Variant	rs2804631
Chromosome Location	chr10:38690515-38690516
allele	A/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	POLR2A	chr10:38690479-38691018	HepG2	liver:	n/a	n/a
2	HEY1	chr10:38690450-38693063	HepG2	liver:	n/a	n/a
3	POLR2A	chr10:38689909-38693482	GM12892	blood:	n/a	n/a
4	POLR2A	chr10:38689987-38693615	GM12878	blood:	n/a	n/a
5	POLR2A	chr10:38690388-38690788	HepG2	liver:	n/a	n/a
6	POLR2A	chr10:38690471-38690646	MCF-7	breast:	n/a	n/a
7	POLR2A	chr10:38690502-38690884	MCF-7	breast:	n/a	n/a

Variant related genes	Relation type
SEPT7P9	TF binding region

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

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs17595292	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs17611180	0.83[ASN][1000 genomes]
rs1892144	0.80[ASN][1000 genomes]
rs2145672	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2754353	0.80[ASN][1000 genomes]
rs2754370	0.80[ASN][1000 genomes]
rs2754495	0.80[AMR][1000 genomes]
rs2800473	0.80[ASN][1000 genomes]
rs2804624	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2804632	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2804639	0.81[AMR][1000 genomes]
rs2804641	0.80[ASN][1000 genomes]
rs2804677	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4934948	0.84[ASN][1000 genomes]
rs61837215	0.87[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs6482064	0.81[EUR][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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2804631	HSD17B7///HSD17B7P2///LOC730412	Cis_1M	lymphoblastoid	RTeQTL
rs2804631	ZNF37A///ZNF37B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:38685600-38691000	Weak transcription	Monocytes-CD14+_RO01746	blood
2	chr10:38690000-38692600	Active TSS	HepG2	liver
3	chr10:38690400-38690600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr10:38690400-38690600	Enhancers	Brain Substantia Nigra	brain
5	chr10:38690400-38690800	Enhancers	Primary T helper cells PMA-I stimulated	--
6	chr10:38690400-38690800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr10:38690400-38690800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
8	chr10:38690400-38690800	Enhancers	Right Ventricle	heart
9	chr10:38690400-38691000	Enhancers	Primary B cells from cord blood	blood
10	chr10:38690400-38691000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr10:38690400-38691000	Active TSS	Skeletal Muscle Male	skeletal muscle
12	chr10:38690400-38691000	Flanking Active TSS	Dnd41	blood
13	chr10:38690400-38692600	Active TSS	Duodenum Mucosa	Duodenum
14	chr10:38690400-38692600	Active TSS	Pancreatic Islets	Pancreatic Islet
15	chr10:38690400-38692600	Active TSS	Pancreas	Pancrea
16	chr10:38690400-38692600	Active TSS	Rectal Mucosa Donor 31	rectum
17	chr10:38690400-38692800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr10:38690400-38692800	Active TSS	Primary hematopoietic stem cells short term culture	blood
19	chr10:38690400-38692800	Active TSS	Fetal Intestine Small	intestine
20	chr10:38690400-38692800	Active TSS	GM12878-XiMat	blood
21	chr10:38690400-38693000	Active TSS	Liver	Liver

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