Variant report

Variant	rs12128789
Chromosome Location	chr1:212852832-212852833
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:212817511..212819084-chr1:212851908..212854150,2	K562	blood:
2	chr1:212782111..212784308-chr1:212852727..212855558,2	MCF-7	breast:
3	chr1:212851040..212855618-chr1:212856353..212859707,5	MCF-7	breast:
4	chr1:212780820..212783342-chr1:212851075..212852900,2	K562	blood:
5	chr1:212847538..212850191-chr1:212852338..212855391,3	K562	blood:

Variant related genes	Relation type
ENSG00000162772	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs12133919	0.87[EUR][1000 genomes]
rs1995689	0.87[EUR][1000 genomes]
rs2174782	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2221593	1.00[CEU][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs2233925	0.87[EUR][1000 genomes]
rs2456812	0.86[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2492789	0.88[ASN][1000 genomes]
rs2501850	0.88[ASN][1000 genomes]
rs2501851	0.88[ASN][1000 genomes]
rs2501852	0.85[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2501857	0.86[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs3754482	0.84[EUR][1000 genomes]
rs3768547	1.00[CEU][hapmap];0.81[MEX][hapmap];0.90[TSI][hapmap];0.87[EUR][1000 genomes]
rs73079851	0.83[EUR][1000 genomes]
rs7533434	0.87[EUR][1000 genomes]
rs906365	1.00[JPT][hapmap];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv549139	chr1:212332294-212876902	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
2	nsv1013110	chr1:212555764-212948092	Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
3	nsv535287	chr1:212555764-212948092	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
4	nsv428588	chr1:212705588-212862875	Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	78 gene(s)	inside rSNPs	diseases
5	esv1829918	chr1:212828460-212874731	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv160457	chr1:212847260-212854762	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12128789	BATF3	cis	brain	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212842200-212854400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr1:212845600-212854000	Weak transcription	A549	lung
3	chr1:212850600-212854800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr1:212850800-212854200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr1:212851000-212853400	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr1:212851600-212856200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr1:212851600-212856800	Weak transcription	Fetal Thymus	thymus
8	chr1:212851800-212853000	Enhancers	Primary B cells from peripheral blood	blood
9	chr1:212851800-212853200	Flanking Active TSS	GM12878-XiMat	blood
10	chr1:212851800-212856000	Weak transcription	Adipose Nuclei	Adipose
11	chr1:212851800-212856800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr1:212852200-212855400	Weak transcription	Brain Hippocampus Middle	brain
13	chr1:212852200-212855400	Weak transcription	Fetal Muscle Leg	muscle
14	chr1:212852400-212854000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr1:212852400-212855400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr1:212852600-212853000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
17	chr1:212852600-212854000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr1:212852600-212855400	Enhancers	Monocytes-CD14+_RO01746	blood
19	chr1:212852600-212856200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr1:212852800-212855400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr1:212852800-212856000	Weak transcription	Spleen	Spleen

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