Variant report

Variant	rs2291855
Chromosome Location	chr12:57410191-57410192
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:57408746..57411435-chr12:57431468..57433360,2	K562	blood:
2	chr12:57144135..57146956-chr12:57408791..57411536,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZBTB39-1	chr12:57410171-57410313	NONHSAT028864
2	lnc-ZBTB39-1	chr12:57410171-57410344	NR_033654

Variant related genes	Relation type
ENSG00000166866	Chromatin interaction
ENSG00000025423	Chromatin interaction
ENSG00000198056	Chromatin interaction

Extended variants
information (count: 115 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:111)

rs_ID	r²[population]
rs10400412	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10400555	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1044939	1.00[CHB][hapmap];0.88[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10506347	0.88[AMR][1000 genomes]
rs10506350	0.90[CHB][hapmap];0.86[JPT][hapmap];0.96[ASN][1000 genomes]
rs10506351	1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1072670	0.89[CHB][hapmap];0.88[JPT][hapmap];0.88[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11832487	0.91[ASN][1000 genomes]
rs11834851	0.91[CHB][hapmap];0.88[JPT][hapmap];0.94[ASN][1000 genomes]
rs11834856	0.94[ASN][1000 genomes]
rs11836517	0.94[ASN][1000 genomes]
rs12099695	0.90[CHB][hapmap];0.86[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12810024	0.80[CHB][hapmap];0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12810837	0.93[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12812499	0.92[ASN][1000 genomes]
rs12815538	0.94[ASN][1000 genomes]
rs12818342	0.96[ASN][1000 genomes]
rs12824682	0.94[ASN][1000 genomes]
rs12825752	0.81[ASN][1000 genomes]
rs12827039	0.94[ASN][1000 genomes]
rs12827286	0.90[ASN][1000 genomes]
rs1552245	1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17119301	0.90[CHB][hapmap];0.86[JPT][hapmap];0.95[ASN][1000 genomes]
rs17119327	1.00[CHB][hapmap];0.86[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]
rs17119330	1.00[CHB][hapmap];0.86[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]
rs17119344	1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17119352	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17119386	1.00[CHB][hapmap];0.86[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17119388	1.00[CHB][hapmap];0.86[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17119390	1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17119407	1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17119416	0.82[CHB][hapmap];0.86[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17119418	0.82[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1843311	0.94[ASN][1000 genomes]
rs1843312	0.94[ASN][1000 genomes]
rs1843313	0.94[ASN][1000 genomes]
rs2167306	0.94[ASN][1000 genomes]
rs2270736	1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2270737	1.00[CHB][hapmap];0.86[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2270739	1.00[CHB][hapmap];0.88[JPT][hapmap];0.94[ASN][1000 genomes]
rs2279373	0.90[CHB][hapmap];0.86[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2279743	0.90[CHB][hapmap];0.86[JPT][hapmap];0.95[ASN][1000 genomes]
rs2371717	1.00[CHB][hapmap];0.86[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28589663	0.96[ASN][1000 genomes]
rs2888139	0.92[ASN][1000 genomes]
rs3024974	0.80[CHB][hapmap]
rs34186462	0.94[ASN][1000 genomes]
rs34253098	0.94[ASN][1000 genomes]
rs34359134	0.94[ASN][1000 genomes]
rs34762603	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34969650	0.94[ASN][1000 genomes]
rs35034299	0.94[ASN][1000 genomes]
rs35243318	0.94[ASN][1000 genomes]
rs35493121	0.90[CHB][hapmap];0.86[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3782329	1.00[CHB][hapmap];0.88[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3782330	1.00[CHB][hapmap];0.86[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3803018	1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3894415	0.95[ASN][1000 genomes]
rs4016338	1.00[CHB][hapmap];0.86[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4039	1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4143085	1.00[CHB][hapmap];0.88[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56128678	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56270558	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56354404	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57056392	0.94[ASN][1000 genomes]
rs57129030	0.94[ASN][1000 genomes]
rs57351760	0.91[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs57558853	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58298943	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58389529	0.95[ASN][1000 genomes]
rs60258120	0.92[ASN][1000 genomes]
rs60273384	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60380217	0.94[ASN][1000 genomes]
rs61504157	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67476535	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67771054	0.94[ASN][1000 genomes]
rs67844278	0.95[ASN][1000 genomes]
rs68126184	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs697222	0.83[ASN][1000 genomes]
rs7135297	0.84[ASN][1000 genomes]
rs7136770	0.90[CHB][hapmap];0.86[JPT][hapmap];0.97[ASN][1000 genomes]
rs71461303	0.91[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs72482268	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7298475	0.82[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73114426	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73114428	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73114434	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73114436	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73114437	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73114446	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73114452	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73114457	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73114459	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73114467	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73114468	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73114472	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73116494	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73116501	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73118413	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73131120	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs733629	1.00[CHB][hapmap];0.86[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]
rs746049	0.90[CHB][hapmap];0.86[JPT][hapmap];0.94[ASN][1000 genomes]
rs7487948	0.94[ASN][1000 genomes]
rs754398	0.99[ASN][1000 genomes]
rs755221	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7956166	0.94[ASN][1000 genomes]
rs7961920	1.00[CHB][hapmap];0.86[JPT][hapmap];0.94[ASN][1000 genomes]
rs7962771	0.82[CHB][hapmap];0.86[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7969312	0.94[ASN][1000 genomes]
rs7972615	1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs901068	0.90[CHB][hapmap];0.86[JPT][hapmap];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1040850	chr12:57055011-57679209	Strong transcription Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	181 gene(s)	inside rSNPs	diseases
2	nsv428590	chr12:57329214-57527358	Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
3	nsv832428	chr12:57340609-57535694	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
4	nsv559022	chr12:57394123-57410389	Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57405200-57410200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr12:57406800-57412600	Weak transcription	Primary T helper cells fromperipheralblood	blood
3	chr12:57407200-57412200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr12:57409000-57412400	Weak transcription	Primary T helper cells PMA-I stimulated	--
5	chr12:57409400-57410400	Enhancers	Placenta	Placenta
6	chr12:57409400-57410600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr12:57409600-57410200	Enhancers	Placenta Amnion	Placenta Amnion
8	chr12:57409600-57410400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr12:57409800-57410200	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
10	chr12:57409800-57410200	Active TSS	Brain Germinal Matrix	brain
11	chr12:57409800-57410400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
12	chr12:57409800-57410400	Flanking Active TSS	K562	blood
13	chr12:57409800-57410600	Enhancers	H9 Cell Line	embryonic stem cell
14	chr12:57409800-57411000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr12:57409800-57413800	Weak transcription	Fetal Thymus	thymus
16	chr12:57410000-57410200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr12:57410000-57410200	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr12:57410000-57410200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
19	chr12:57410000-57410200	Enhancers	HUES64 Cell Line	embryonic stem cell
20	chr12:57410000-57410200	Bivalent/Poised TSS	HepG2	liver
21	chr12:57410000-57410400	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
22	chr12:57410000-57410400	Flanking Active TSS	H1 Cell Line	embryonic stem cell
23	chr12:57410000-57410400	Active TSS	iPS-18 Cell Line	embryonic stem cell
24	chr12:57410000-57410400	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell

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