Variant report

Variant	rs6883872
Chromosome Location	chr5:89933134-89933135
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	JUN	chr5:89933025-89933225	K562	blood:	n/a	n/a
2	POLR2A	chr5:89933055-89933236	MCF10A-Er-Src	breast:	n/a	n/a
3	EP300	chr5:89933077-89933283	GM12878	blood:	n/a	n/a
4	RCOR1	chr5:89932797-89933174	K562	blood:	n/a	n/a
5	ARID3A	chr5:89932587-89935259	K562	blood:	n/a	n/a
6	ZNF143	chr5:89932757-89933158	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:89904239..89908604-chr5:89932898..89936068,3	K562	blood:

Variant related genes	Relation type
GPR98	TF binding region

Extended variants
information (count: 101 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10036980	0.92[CHB][hapmap];0.91[JPT][hapmap]
rs10043836	1.00[CHB][hapmap];0.92[JPT][hapmap];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10058765	1.00[CHB][hapmap];0.92[JPT][hapmap];0.92[ASN][1000 genomes]
rs10060427	1.00[CHB][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs10062714	1.00[CHB][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs10062924	1.00[CHB][hapmap];0.92[JPT][hapmap];0.92[ASN][1000 genomes]
rs10067181	0.92[JPT][hapmap]
rs10068473	0.91[JPT][hapmap]
rs10072105	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1028191	1.00[CHB][hapmap];0.91[JPT][hapmap];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1028192	1.00[CHB][hapmap];0.91[JPT][hapmap];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1033290	1.00[CHB][hapmap];0.91[JPT][hapmap];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10462342	0.83[JPT][hapmap]
rs10473936	0.82[ASN][1000 genomes]
rs10514327	0.83[JPT][hapmap]
rs10514333	0.84[CHB][hapmap];0.90[JPT][hapmap]
rs10942597	0.92[JPT][hapmap]
rs10942605	0.91[JPT][hapmap]
rs10942606	0.92[CHB][hapmap];0.91[JPT][hapmap]
rs1160121	0.91[JPT][hapmap]
rs11741740	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12187830	0.88[ASN][1000 genomes]
rs12188928	0.91[JPT][hapmap]
rs12516985	1.00[CHB][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs12655180	0.82[JPT][hapmap]
rs13185955	0.92[JPT][hapmap]
rs1533603	0.92[CHB][hapmap];0.92[JPT][hapmap]
rs1673378	0.81[CHB][hapmap];0.92[JPT][hapmap]
rs1673379	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16868957	1.00[CHB][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs1700510	1.00[CHB][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs1700511	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1878878	1.00[CHB][hapmap];0.91[JPT][hapmap];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1988788	0.86[ASN][1000 genomes]
rs1993474	0.91[JPT][hapmap]
rs2176624	0.93[CHB][hapmap];0.92[JPT][hapmap]
rs2222242	0.92[CHB][hapmap];0.92[JPT][hapmap]
rs2366771	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2366773	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2366774	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.83[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2366777	1.00[CHB][hapmap];0.91[JPT][hapmap];0.82[YRI][hapmap];0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28517617	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28550273	0.92[ASN][1000 genomes]
rs3805483	0.82[JPT][hapmap]
rs3927265	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs4379236	0.92[ASN][1000 genomes]
rs4574581	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs474800	0.84[ASN][1000 genomes]
rs490812	0.92[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs491241	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4916681	1.00[CHB][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs4916682	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4916684	1.00[CHB][hapmap];0.91[JPT][hapmap];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4916686	0.93[CHB][hapmap];0.92[JPT][hapmap]
rs4916813	1.00[CHB][hapmap];0.91[JPT][hapmap];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4916814	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4916815	0.91[JPT][hapmap]
rs498491	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs499148	0.92[JPT][hapmap]
rs501640	0.81[ASN][1000 genomes]
rs502596	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs552314	0.84[ASN][1000 genomes]
rs587818	0.80[ASN][1000 genomes]
rs603015	0.92[JPT][hapmap]
rs617379	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs618355	0.90[JPT][hapmap]
rs623761	0.84[ASN][1000 genomes]
rs637442	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6452906	0.92[CHB][hapmap];0.91[JPT][hapmap]
rs645652	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs648430	0.92[JPT][hapmap]
rs666659	0.82[ASN][1000 genomes]
rs6861525	0.85[ASN][1000 genomes]
rs6863710	1.00[CHB][hapmap];0.91[JPT][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6870337	0.83[ASN][1000 genomes]
rs6878917	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6881412	0.92[CHB][hapmap];0.91[JPT][hapmap]
rs6888355	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs688956	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs688960	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6891275	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6897910	0.82[JPT][hapmap]
rs6898209	1.00[CHB][hapmap];0.91[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7703530	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7703588	0.92[CHB][hapmap];0.92[JPT][hapmap]
rs7721198	0.92[CHB][hapmap];0.90[JPT][hapmap]
rs7723259	0.92[CHB][hapmap];0.92[JPT][hapmap]
rs7724806	0.92[CHB][hapmap];0.92[JPT][hapmap]
rs7726624	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7729703	1.00[CHB][hapmap];0.92[JPT][hapmap];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7732169	0.91[JPT][hapmap]
rs9283788	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9293550	0.93[CHB][hapmap];0.92[JPT][hapmap]
rs963866	1.00[CHB][hapmap];0.92[JPT][hapmap];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs977906	1.00[CHB][hapmap];0.92[JPT][hapmap];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9790907	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	nsv531965	chr5:89886550-90145002	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:89918000-89950600	Weak transcription	Pancreas	Pancrea
2	chr5:89919600-89936400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr5:89925200-89936400	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr5:89925400-89936200	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr5:89925400-89938600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr5:89928800-89940000	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr5:89928800-89941000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr5:89929000-89933400	Weak transcription	K562	blood
9	chr5:89929000-89935800	Weak transcription	Brain Germinal Matrix	brain
10	chr5:89929000-89936400	Weak transcription	Fetal Brain Female	brain
11	chr5:89929000-89936600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr5:89929000-89940400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr5:89929000-89948600	Weak transcription	Brain Anterior Caudate	brain
14	chr5:89930400-89935800	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr5:89931200-89935200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr5:89931200-89935600	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chr5:89931200-89935800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr5:89931600-89935200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr5:89931800-89934600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr5:89932400-89935200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
21	chr5:89932600-89935400	Strong transcription	HUES48 Cell Line	embryonic stem cell

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