Variant report

Variant	rs10514860
Chromosome Location	chr5:58824020-58824021
allele	A/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	GATA3	chr5:58823740-58824647	SK-N-SH	brain:	n/a	n/a
2	POLR2A	chr5:58823745-58824535	PFSK-1	brain:	n/a	n/a
3	GATA3	chr5:58823953-58824098	SH-SY5Y	brain:	n/a	n/a

Variant related genes	Relation type
NDUFB4P2	TF binding region

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11949561	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12187079	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12187448	0.83[CEU][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17728654	1.00[JPT][hapmap]
rs17740749	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17740767	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17741233	0.83[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17795596	1.00[JPT][hapmap]
rs17795692	1.00[JPT][hapmap]
rs17796040	1.00[JPT][hapmap]
rs17796824	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17797601	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2081093	0.84[CEU][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2098699	1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4326095	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4551023	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56075449	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56396168	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6861969	0.84[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs72767794	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72767801	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72767802	0.84[EUR][1000 genomes]
rs72769704	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7717821	1.00[JPT][hapmap]
rs7729912	1.00[JPT][hapmap]
rs7737908	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv598254	chr5:58715782-58923601	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv881706	chr5:58730111-58865857	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv1031631	chr5:58783629-59015470	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58815400-58830400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr5:58819000-58832600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr5:58820000-58831400	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr5:58820800-58824600	Weak transcription	Psoas Muscle	Psoas
5	chr5:58821000-58828600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr5:58822200-58838800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr5:58822600-58824400	Weak transcription	HSMMtube	muscle
8	chr5:58822800-58824200	Weak transcription	Fetal Intestine Large	intestine
9	chr5:58822800-58824600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr5:58822800-58837600	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr5:58823000-58838200	Weak transcription	Fetal Brain Male	brain
12	chr5:58823400-58824800	Enhancers	Muscle Satellite Cultured Cells	--
13	chr5:58823400-58825400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr5:58823600-58824200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr5:58823600-58824800	Enhancers	HUES6 Cell Line	embryonic stem cell
16	chr5:58823600-58825000	Enhancers	HUVEC	blood vessel
17	chr5:58823600-58825400	Enhancers	Skeletal Muscle Female	skeletal muscle
18	chr5:58823800-58824200	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr5:58823800-58824200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
20	chr5:58823800-58824400	Enhancers	Brain Substantia Nigra	brain
21	chr5:58823800-58824600	Weak transcription	Colon Smooth Muscle	Colon
22	chr5:58823800-58824800	Enhancers	HUES48 Cell Line	embryonic stem cell
23	chr5:58823800-58824800	Enhancers	Stomach Mucosa	stomach
24	chr5:58823800-58824800	Enhancers	Hela-S3	cervix
25	chr5:58823800-58825000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr5:58823800-58825000	Enhancers	HSMM	muscle
27	chr5:58823800-58826000	Enhancers	Skeletal Muscle Male	skeletal muscle
28	chr5:58824000-58824200	Enhancers	Duodenum Mucosa	Duodenum
29	chr5:58824000-58824200	Enhancers	Rectal Mucosa Donor 31	rectum
30	chr5:58824000-58824800	Enhancers	iPS-18 Cell Line	embryonic stem cell
31	chr5:58824000-58824800	Enhancers	Fetal Intestine Small	intestine
32	chr5:58824000-58824800	Transcr. at gene 5' and 3'	A549	lung

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