Variant report

Variant	rs12460721
Chromosome Location	chr19:36477855-36477856
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:36468262..36470231-chr19:36477394..36478967,2	MCF-7	breast:
2	chr19:36476284..36477948-chr19:36485928..36488344,2	K562	blood:
3	chr19:36476612..36479573-chr19:36497670..36500515,2	MCF-7	breast:
4	chr19:36476028..36480539-chr19:36483791..36486767,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000205138	Chromatin interaction
ENSG00000181392	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1043822	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10469279	0.94[CHB][hapmap];0.94[CHD][hapmap];0.92[JPT][hapmap];0.89[ASN][1000 genomes]
rs12462677	0.94[CHB][hapmap];0.84[JPT][hapmap];0.90[ASN][1000 genomes]
rs12462868	0.86[ASN][1000 genomes]
rs17720402	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2073893	0.94[CHB][hapmap];0.94[CHD][hapmap];0.92[JPT][hapmap];0.90[ASN][1000 genomes]
rs2285423	0.82[ASN][1000 genomes]
rs2285424	0.80[CEU][hapmap];0.94[CHB][hapmap];0.91[CHD][hapmap];0.92[JPT][hapmap];0.91[ASN][1000 genomes]
rs4458134	0.93[ASN][1000 genomes]
rs4806245	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.92[JPT][hapmap];0.97[ASN][1000 genomes]
rs4806247	0.94[CHB][hapmap];0.81[JPT][hapmap];0.90[ASN][1000 genomes]
rs7256169	0.88[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.82[YRI][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7258897	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	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
7	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
8	nsv911641	chr19:36473677-36536938	Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Weak transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12460721	PSG1	cis	cerebellum	SCAN
rs12460721	PLEKHG2	cis	cerebellum	SCAN

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36476400-36478000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
2	chr19:36477000-36478200	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr19:36477000-36478400	Enhancers	Spleen	Spleen
4	chr19:36477200-36478000	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr19:36477200-36478000	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr19:36477200-36478200	Enhancers	Pancreas	Pancrea
7	chr19:36477400-36478600	Active TSS	H9 Cell Line	embryonic stem cell
8	chr19:36477400-36478600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
9	chr19:36477400-36478600	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
10	chr19:36477400-36478800	Bivalent Enhancer	Placenta	Placenta
11	chr19:36477600-36478000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
12	chr19:36477600-36478000	Flanking Active TSS	Primary B cells from peripheral blood	blood
13	chr19:36477600-36478000	Bivalent Enhancer	Brain Cingulate Gyrus	brain
14	chr19:36477600-36478000	Bivalent/Poised TSS	HepG2	liver
15	chr19:36477600-36478000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
16	chr19:36477600-36478200	Flanking Active TSS	Primary B cells from cord blood	blood
17	chr19:36477600-36478200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr19:36477600-36478200	Bivalent/Poised TSS	Brain Germinal Matrix	brain
19	chr19:36477600-36478200	Enhancers	GM12878-XiMat	blood
20	chr19:36477600-36478400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
21	chr19:36477600-36478400	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
22	chr19:36477600-36478600	Active TSS	HUES48 Cell Line	embryonic stem cell
23	chr19:36477600-36478600	Enhancers	Primary hematopoietic stem cells	blood
24	chr19:36477600-36478600	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
25	chr19:36477600-36478600	Bivalent/Poised TSS	Fetal Brain Female	brain
26	chr19:36477600-36478800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
27	chr19:36477600-36478800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
28	chr19:36477600-36478800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr19:36477800-36478000	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
30	chr19:36477800-36478000	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr19:36477800-36478000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr19:36477800-36478000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
33	chr19:36477800-36478000	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
34	chr19:36477800-36478000	Flanking Bivalent TSS/Enh	Primary T cells from cord blood	blood
35	chr19:36477800-36478000	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
36	chr19:36477800-36478000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
37	chr19:36477800-36478000	Flanking Bivalent TSS/Enh	Primary T helper naive cells fromperipheralblood	blood
38	chr19:36477800-36478000	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
39	chr19:36477800-36478000	Flanking Bivalent TSS/Enh	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr19:36477800-36478000	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr19:36477800-36478000	Flanking Bivalent TSS/Enh	Brain Angular Gyrus	brain
42	chr19:36477800-36478000	Bivalent Enhancer	Fetal Heart	heart
43	chr19:36477800-36478000	Bivalent Enhancer	Fetal Lung	lung
44	chr19:36477800-36478000	Bivalent Enhancer	Fetal Muscle Leg	muscle
45	chr19:36477800-36478000	Bivalent Enhancer	Fetal Stomach	stomach
46	chr19:36477800-36478000	Bivalent/Poised TSS	Placenta Amnion	Placenta Amnion
47	chr19:36477800-36478000	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 31	rectum
48	chr19:36477800-36478000	Flanking Active TSS	Right Atrium	heart
49	chr19:36477800-36478000	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
50	chr19:36477800-36478000	Bivalent/Poised TSS	Small Intestine	intestine

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