Variant report

Variant	rs12461927
Chromosome Location	chr19:35800077-35800078
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RCOR1	chr19:35799869-35801133	K562	blood:	n/a	n/a
2	POLR2A	chr19:35799932-35801269	K562	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr19:35796764..35800582-chr19:36132788..36136056,3	K562	blood:
2	chr19:35798397..35800415-chr19:35842184..35843828,2	MCF-7	breast:
3	chr19:35757193..35760230-chr19:35795583..35800096,4	K562	blood:
4	chr19:35797829..35800128-chr19:35823862..35825668,2	MCF-7	breast:
5	chr19:35757352..35763490-chr19:35798817..35804347,10	MCF-7	breast:
6	chr19:35794875..35797641-chr19:35798078..35800124,2	MCF-7	breast:
7	chr19:35781735..35783754-chr19:35799663..35801226,2	MCF-7	breast:
8	chr19:35738675..35740393-chr19:35799543..35801412,2	MCF-7	breast:
9	chr19:35755149..35764508-chr19:35799437..35813142,44	MCF-7	breast:

No data

Variant related genes	Relation type
MAG	TF binding region
ENSG00000105698	Chromatin interaction
ENSG00000126266	Chromatin interaction
ENSG00000105699	Chromatin interaction
ENSG00000105672	Chromatin interaction
ENSG00000105695	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1126770	0.81[ASN][1000 genomes]
rs11666282	0.94[CEU][hapmap]
rs11670792	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.92[MEX][hapmap];0.94[MKK][hapmap];0.92[TSI][hapmap];0.90[YRI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11673522	0.94[CEU][hapmap]
rs12463142	1.00[CEU][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17637981	0.94[CEU][hapmap];0.86[EUR][1000 genomes]
rs17705279	0.89[CEU][hapmap];0.89[GIH][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs1811170	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2285447	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2301600	0.91[LWK][hapmap];0.90[YRI][hapmap]
rs720308	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.93[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs720309	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73031717	0.90[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	nsv1060100	chr19:35658505-36170042	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
3	nsv543993	chr19:35658505-36170042	Enhancers Strong transcription Active TSS Weak transcription Bivalent Enhancer Flanking 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	107 gene(s)	inside rSNPs	diseases
4	nsv510765	chr19:35708226-35890668	Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
5	esv2758497	chr19:35711078-35887113	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
6	esv2758758	chr19:35711078-35887113	Bivalent Enhancer Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
7	nsv911618	chr19:35734107-35807845	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
8	nsv833810	chr19:35782588-35971959	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases
9	nsv9711	chr19:35797190-35805196	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	n/a
10	esv1006379	chr19:35798572-35810821	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	n/a

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12461927	HIPK4	cis	parietal	SCAN
rs12461927	CYP2B7P1	cis	parietal	SCAN
rs12461927	PSMC4	cis	cerebellum	SCAN
rs12461927	MYEOV2	trans	cerebellum	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:35774800-35809600	Weak transcription	Right Atrium	heart
2	chr19:35792800-35801400	Genic enhancers	Brain Hippocampus Middle	brain
3	chr19:35794400-35810000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr19:35795000-35800400	Enhancers	HepG2	liver
5	chr19:35796800-35800600	Enhancers	Ovary	ovary
6	chr19:35796800-35801000	Weak transcription	Fetal Thymus	thymus
7	chr19:35797000-35800800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr19:35797200-35802200	Weak transcription	Brain Anterior Caudate	brain
9	chr19:35797600-35804000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr19:35797800-35800200	Enhancers	Fetal Kidney	kidney
11	chr19:35797800-35800800	Genic enhancers	Brain Substantia Nigra	brain
12	chr19:35797800-35809600	Weak transcription	Brain Angular Gyrus	brain
13	chr19:35798000-35801400	Enhancers	Fetal Muscle Trunk	muscle
14	chr19:35798000-35801800	Enhancers	Fetal Stomach	stomach
15	chr19:35798000-35802600	Enhancers	Placenta	Placenta
16	chr19:35798200-35801400	Enhancers	Fetal Muscle Leg	muscle
17	chr19:35798200-35802800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr19:35798200-35811400	Weak transcription	Liver	Liver
19	chr19:35799000-35800400	Weak transcription	GM12878-XiMat	blood
20	chr19:35799200-35801200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr19:35799200-35804000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr19:35799400-35800600	Weak transcription	Spleen	Spleen
23	chr19:35799400-35800800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr19:35799400-35804200	Weak transcription	Primary hematopoietic stem cells	blood
25	chr19:35799600-35801400	Genic enhancers	Brain Cingulate Gyrus	brain
26	chr19:35799600-35803400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
27	chr19:35799800-35801200	Enhancers	Duodenum Mucosa	Duodenum
28	chr19:35800000-35800200	Enhancers	Primary B cells from peripheral blood	blood
29	chr19:35800000-35800400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr19:35800000-35801000	Enhancers	Lung	lung
31	chr19:35800000-35801000	Enhancers	Hela-S3	cervix
32	chr19:35800000-35801600	Flanking Active TSS	K562	blood
33	chr19:35800000-35801800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr19:35800000-35801800	Flanking Active TSS	Fetal Lung	lung
35	chr19:35800000-35803800	Strong transcription	Brain Inferior Temporal Lobe	brain
36	chr19:35800000-35804000	Weak transcription	Primary B cells from cord blood	blood

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