Variant report

Variant	rs1700510
Chromosome Location	chr5:89857264-89857265
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:89768826..89771669-chr5:89856234..89860073,3	K562	blood:
2	chr5:89854731..89856596-chr5:89856787..89860606,4	K562	blood:
3	chr5:89828910..89830955-chr5:89855867..89858552,2	MCF-7	breast:
4	chr5:89856963..89860302-chr5:89865083..89868215,3	MCF-7	breast:
5	chr5:89703976..89707575-chr5:89854064..89857316,4	K562	blood:
6	chr5:89705231..89707575-chr5:89854422..89857316,5	K562	blood:
7	chr5:89855529..89859468-chr5:89877001..89881365,3	MCF-7	breast:
8	chr5:89854805..89859362-chr5:89860971..89864483,4	K562	blood:
9	chr5:89829601..89833585-chr5:89854929..89859978,5	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000176055	Chromatin interaction
ENSG00000153140	Chromatin interaction
ENSG00000255647	Chromatin interaction
ENSG00000113356	Chromatin interaction

Extended variants
information (count: 104 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs10036980	0.92[CHB][hapmap];0.83[JPT][hapmap]
rs10043836	1.00[CHB][hapmap];0.84[JPT][hapmap]
rs10058765	1.00[CHB][hapmap];0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs10060427	1.00[CHB][hapmap];0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs10062714	1.00[CHB][hapmap];0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs10062924	1.00[CHB][hapmap];0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs10067181	0.84[JPT][hapmap]
rs10068473	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs10072105	1.00[CHB][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs1028191	1.00[CHB][hapmap];0.83[JPT][hapmap]
rs1028192	1.00[CHB][hapmap];0.83[JPT][hapmap]
rs1033290	1.00[CHB][hapmap];0.83[JPT][hapmap]
rs10462342	0.80[CEU][hapmap]
rs10473936	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1047787	0.84[EUR][1000 genomes]
rs10514327	0.83[CEU][hapmap];0.81[CHB][hapmap]
rs10514328	0.87[ASN][1000 genomes]
rs10514333	0.85[CHB][hapmap];0.83[JPT][hapmap]
rs10942597	0.96[CEU][hapmap];0.81[CHB][hapmap];0.83[JPT][hapmap];0.83[EUR][1000 genomes]
rs10942605	0.83[JPT][hapmap]
rs10942606	0.92[CHB][hapmap];0.83[JPT][hapmap]
rs1160121	0.83[JPT][hapmap]
rs11741740	0.93[ASN][1000 genomes]
rs12188928	0.83[JPT][hapmap]
rs12516985	1.00[CHB][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs12655180	0.83[YRI][hapmap]
rs13182165	0.87[EUR][1000 genomes]
rs13185955	0.96[CEU][hapmap];0.81[CHB][hapmap];0.83[JPT][hapmap];0.86[EUR][1000 genomes]
rs1533603	0.93[CHB][hapmap];0.84[JPT][hapmap]
rs1673378	0.96[CEU][hapmap];0.81[CHB][hapmap];0.83[JPT][hapmap];0.86[EUR][1000 genomes]
rs1673379	0.93[CHB][hapmap];0.92[JPT][hapmap];0.85[ASN][1000 genomes]
rs16868957	1.00[CHB][hapmap];0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs1700511	0.93[CHB][hapmap];0.92[JPT][hapmap];0.87[ASN][1000 genomes]
rs1812737	0.87[EUR][1000 genomes]
rs1878878	1.00[CHB][hapmap];0.83[JPT][hapmap]
rs1993474	0.91[JPT][hapmap]
rs2176624	0.93[CHB][hapmap];0.84[JPT][hapmap]
rs2222242	0.93[CHB][hapmap];0.84[JPT][hapmap]
rs2366771	1.00[CHB][hapmap];0.92[JPT][hapmap]
rs2366773	1.00[CHB][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs2366774	1.00[CHB][hapmap];0.84[JPT][hapmap];0.84[ASN][1000 genomes]
rs2366777	1.00[CHB][hapmap];0.83[JPT][hapmap]
rs28550273	0.83[ASN][1000 genomes]
rs3087840	0.84[EUR][1000 genomes]
rs3805483	0.81[CHB][hapmap]
rs3927265	0.85[CHB][hapmap];0.83[JPT][hapmap]
rs4379236	0.83[ASN][1000 genomes]
rs474800	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs490812	0.92[CHB][hapmap];0.92[JPT][hapmap];0.87[ASN][1000 genomes]
rs491241	0.90[ASN][1000 genomes]
rs4916681	1.00[CHB][hapmap];0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs4916684	1.00[CHB][hapmap];0.83[JPT][hapmap]
rs4916686	0.93[CHB][hapmap];0.84[JPT][hapmap]
rs4916813	1.00[CHB][hapmap];0.83[JPT][hapmap]
rs4916815	0.82[JPT][hapmap]
rs498491	1.00[CHB][hapmap];0.92[JPT][hapmap];0.91[ASN][1000 genomes]
rs499148	0.96[CEU][hapmap];0.81[CHB][hapmap];0.83[JPT][hapmap];0.82[YRI][hapmap];0.88[EUR][1000 genomes]
rs501640	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs502596	0.93[CHB][hapmap];0.92[JPT][hapmap];0.88[ASN][1000 genomes]
rs552314	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs558809	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs587818	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs603015	0.96[CEU][hapmap];0.81[CHB][hapmap];0.83[JPT][hapmap];0.86[EUR][1000 genomes]
rs603870	0.87[EUR][1000 genomes]
rs616379	0.85[EUR][1000 genomes]
rs617379	1.00[CHB][hapmap];0.92[JPT][hapmap];0.89[ASN][1000 genomes]
rs618355	0.96[CEU][hapmap];0.81[CHB][hapmap];0.83[JPT][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs623761	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs637442	0.93[CHB][hapmap];0.92[JPT][hapmap];0.87[ASN][1000 genomes]
rs6452906	0.92[CHB][hapmap];0.83[JPT][hapmap]
rs645652	1.00[CHB][hapmap];0.92[JPT][hapmap];0.91[ASN][1000 genomes]
rs648430	0.96[CEU][hapmap];0.81[CHB][hapmap];0.83[JPT][hapmap];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs666659	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6863710	1.00[CHB][hapmap];0.83[JPT][hapmap]
rs6878917	1.00[CHB][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs6881412	0.92[CHB][hapmap];0.83[JPT][hapmap]
rs6883872	1.00[CHB][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs6888355	1.00[CHB][hapmap];0.91[JPT][hapmap];0.93[ASN][1000 genomes]
rs688956	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.85[YRI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs688960	1.00[CHB][hapmap];0.92[JPT][hapmap];0.91[ASN][1000 genomes]
rs6897910	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs6898209	1.00[CHB][hapmap];0.83[JPT][hapmap]
rs7703588	0.85[CHB][hapmap];0.84[JPT][hapmap]
rs7716979	0.84[EUR][1000 genomes]
rs7717423	0.86[EUR][1000 genomes]
rs7721198	0.92[CHB][hapmap];0.81[JPT][hapmap]
rs7723259	0.92[CHB][hapmap];0.83[JPT][hapmap]
rs7724806	0.92[CHB][hapmap];0.84[JPT][hapmap]
rs7726624	1.00[CHB][hapmap];0.92[JPT][hapmap];0.86[ASN][1000 genomes]
rs7729703	1.00[CHB][hapmap];0.84[JPT][hapmap]
rs7732169	0.83[JPT][hapmap]
rs9283788	0.82[ASN][1000 genomes]
rs9293550	0.93[CHB][hapmap];0.84[JPT][hapmap]
rs963866	1.00[CHB][hapmap];0.84[JPT][hapmap]
rs977906	1.00[CHB][hapmap];0.84[JPT][hapmap]
rs9790907	1.00[CHB][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021142	chr5:89102893-89897826	Active TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv537804	chr5:89102893-89897826	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv432750	chr5:89410113-90137144	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
4	nsv432751	chr5:89457044-90090444	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
5	nsv529544	chr5:89523963-90412409	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
6	nsv882365	chr5:89770768-89882618	Flanking Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	13 gene(s)	inside rSNPs	diseases
7	nsv882366	chr5:89826726-89894564	Bivalent/Poised TSS Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
8	nsv933668	chr5:89854253-89999672	Strong transcription Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1700510	LYSMD3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:89853600-89857600	Active TSS	H1 Cell Line	embryonic stem cell
2	chr5:89853800-89858000	Active TSS	K562	blood
3	chr5:89854200-89858400	Active TSS	Fetal Brain Female	brain
4	chr5:89855200-89858200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr5:89855200-89871000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr5:89855400-89857600	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
7	chr5:89855400-89857800	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr5:89855400-89858400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr5:89855600-89858200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr5:89855800-89858000	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr5:89856200-89858400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr5:89856200-89860400	Enhancers	ES-I3 Cell Line	embryonic stem cell
13	chr5:89856400-89857600	Enhancers	Pancreatic Islets	Pancreatic Islet
14	chr5:89856400-89858000	Enhancers	Fetal Brain Male	brain
15	chr5:89856400-89859600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
16	chr5:89856400-89859800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr5:89856600-89859800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
18	chr5:89856600-89860200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
19	chr5:89856600-89860400	Enhancers	iPS-15b Cell Line	embryonic stem cell
20	chr5:89856800-89860000	Enhancers	HUES6 Cell Line	embryonic stem cell
21	chr5:89857000-89857400	Flanking Active TSS	Brain Germinal Matrix	brain
22	chr5:89857000-89859000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr5:89857200-89857400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr5:89857200-89858000	Enhancers	iPS-18 Cell Line	embryonic stem cell

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