Variant report

Variant	rs230260
Chromosome Location	chr19:36358563-36358564
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	TCF12	chr19:36358456-36361435	A549	lung:	n/a	chr19:36359844-36359854 chr19:36359284-36359292
2	MXI1	chr19:36358552-36361464	SK-N-SH	brain:	n/a	chr19:36360367-36360382 chr19:36360325-36360340 chr19:36360369-36360384 chr19:36360417-36360432

No.	Distal block	Cell Line	Cell type
1	chr19:36358531..36360792-chr19:36503749..36506105,2	MCF-7	breast:
2	chr19:36208378..36210285-chr19:36358548..36361708,3	K562	blood:
3	chr19:36208185..36209878-chr19:36358146..36361161,3	K562	blood:

Variant related genes	Relation type
APLP1	TF binding region
ENSG00000267698	Chromatin interaction
ENSG00000272333	Chromatin interaction
ENSG00000239382	Chromatin interaction

Extended variants
information (count: 120 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:110)

rs_ID	r²[population]
rs1057265	0.81[EUR][1000 genomes]
rs11084834	1.00[CEU][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs11878444	0.81[EUR][1000 genomes]
rs11878547	0.87[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11880909	1.00[CEU][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs11881358	0.95[EUR][1000 genomes]
rs11881364	0.95[EUR][1000 genomes]
rs11881451	1.00[CEU][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs11882386	0.81[EUR][1000 genomes]
rs16960862	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs16970735	0.95[EUR][1000 genomes]
rs16970737	1.00[CEU][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs16970742	1.00[CEU][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs16970744	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs172985	1.00[CEU][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs1802029	0.86[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2227909	1.00[CEU][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs2242590	0.81[EUR][1000 genomes]
rs230261	1.00[CEU][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs230262	1.00[CEU][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs230263	0.95[EUR][1000 genomes]
rs230264	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs230265	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs230266	0.95[EUR][1000 genomes]
rs230267	0.95[EUR][1000 genomes]
rs230268	0.86[EUR][1000 genomes]
rs230269	0.95[EUR][1000 genomes]
rs2871778	1.00[CEU][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs33964243	0.83[ASN][1000 genomes]
rs34006827	0.95[EUR][1000 genomes]
rs35423326	0.95[EUR][1000 genomes]
rs376240	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs392702	0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs393116	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs401824	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs404299	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs412175	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs417786	0.81[EUR][1000 genomes]
rs437168	1.00[CEU][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes]
rs443186	1.00[CEU][hapmap];0.83[CHD][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs447783	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs55797913	0.95[EUR][1000 genomes]
rs55816190	0.95[EUR][1000 genomes]
rs56264349	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56922307	0.81[EUR][1000 genomes]
rs57053076	0.95[EUR][1000 genomes]
rs57068163	0.81[EUR][1000 genomes]
rs57094555	0.81[EUR][1000 genomes]
rs57516855	0.84[EUR][1000 genomes]
rs57668132	0.95[EUR][1000 genomes]
rs58098901	0.95[EUR][1000 genomes]
rs58109577	0.95[EUR][1000 genomes]
rs58161969	0.81[EUR][1000 genomes]
rs58291714	1.00[EUR][1000 genomes]
rs58422001	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs58504183	0.85[EUR][1000 genomes]
rs58551711	0.85[EUR][1000 genomes]
rs59123406	0.95[EUR][1000 genomes]
rs59399698	0.84[EUR][1000 genomes]
rs59534183	0.84[EUR][1000 genomes]
rs59658571	0.95[EUR][1000 genomes]
rs60073802	0.81[EUR][1000 genomes]
rs60268250	1.00[EUR][1000 genomes]
rs60576074	0.89[EUR][1000 genomes]
rs60869994	1.00[EUR][1000 genomes]
rs60935148	0.85[EUR][1000 genomes]
rs61623584	0.95[EUR][1000 genomes]
rs61660311	0.81[EUR][1000 genomes]
rs619833	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7251744	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7251879	1.00[ASW][hapmap];0.80[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.91[ASN][1000 genomes]
rs7252902	0.81[ASN][1000 genomes]
rs7253040	0.83[ASN][1000 genomes]
rs7253086	0.85[EUR][1000 genomes]
rs7253826	0.83[ASN][1000 genomes]
rs7254113	0.87[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7256433	0.85[EUR][1000 genomes]
rs7257789	0.82[ASW][hapmap];0.83[YRI][hapmap]
rs7258154	0.83[ASN][1000 genomes]
rs7258214	0.90[ASN][1000 genomes]
rs7258909	1.00[ASW][hapmap];1.00[CEU][hapmap];0.80[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73594463	0.82[AMR][1000 genomes]
rs73599539	0.81[EUR][1000 genomes]
rs73599540	0.81[EUR][1000 genomes]
rs73599546	0.81[EUR][1000 genomes]
rs73599565	0.81[EUR][1000 genomes]
rs73599577	0.81[EUR][1000 genomes]
rs73599600	0.85[EUR][1000 genomes]
rs73599602	0.81[EUR][1000 genomes]
rs73928331	0.85[EUR][1000 genomes]
rs73928332	0.95[EUR][1000 genomes]
rs73928333	0.95[EUR][1000 genomes]
rs807660	0.95[EUR][1000 genomes]
rs8105153	0.83[ASN][1000 genomes]
rs8106480	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs8106495	0.87[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs8106732	0.95[EUR][1000 genomes]
rs8108360	0.83[ASN][1000 genomes]
rs8108459	0.83[ASN][1000 genomes]
rs8110231	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs8110868	0.81[EUR][1000 genomes]
rs8110926	0.95[EUR][1000 genomes]
rs8111209	0.95[EUR][1000 genomes]
rs8111348	0.95[EUR][1000 genomes]
rs8111740	0.83[ASN][1000 genomes]
rs8113524	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs8113704	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap];0.88[ASN][1000 genomes]
rs879407	1.00[ASW][hapmap];1.00[CEU][hapmap];0.80[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9749325	0.95[EUR][1000 genomes]
rs9749492	1.00[CEU][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432045	chr19:35556260-36520760	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	nsv911638	chr19:36265508-36537959	Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	esv3526489	chr19:36306483-36741945	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
4	esv3526490	chr19:36306483-36741945	Genic enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
5	esv1831737	chr19:36324324-36690874	Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
6	esv3397651	chr19:36326933-36377725	Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	nsv833812	chr19:36331913-36507594	Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
8	nsv833813	chr19:36341181-36499431	Flanking Active TSS Weak transcription Strong transcription Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
9	nsv911639	chr19:36342909-36365985	Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
10	nsv911640	chr19:36353880-36365985	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36349600-36358800	Weak transcription	Dnd41	blood
2	chr19:36352200-36359000	Weak transcription	Right Atrium	heart
3	chr19:36352800-36358600	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr19:36352800-36358600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr19:36352800-36358600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr19:36353600-36358600	Weak transcription	Fetal Brain Female	brain
7	chr19:36353600-36359400	Weak transcription	Gastric	stomach
8	chr19:36356800-36359000	Weak transcription	Esophagus	oesophagus
9	chr19:36357000-36358600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr19:36357600-36358600	Weak transcription	Pancreas	Pancrea
11	chr19:36358000-36359000	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr19:36358400-36358600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr19:36358400-36358800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr19:36358400-36359000	Enhancers	Fetal Brain Male	brain
15	chr19:36358400-36359400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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