Variant report

Variant	rs12461333
Chromosome Location	chr19:36192905-36192906
allele	C/G
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	MTA3	chr19:36192897-36194080	GM12878	blood:	n/a	n/a
2	POLR2A	chr19:36192900-36194052	GM12892	blood:	n/a	n/a
3	PML	chr19:36192844-36193964	GM12878	blood:	n/a	n/a
4	SP1	chr19:36192879-36194047	A549	lung:	n/a	chr19:36193408-36193429 chr19:36193358-36193379 chr19:36193673-36193687 chr19:36193310-36193322 chr19:36193598-36193611
5	RUNX3	chr19:36192742-36193941	GM12878	blood:	n/a	n/a
6	MAX	chr19:36192847-36194114	A549	lung:	n/a	n/a
7	SIN3AK20	chr19:36192824-36194041	MCF-7	breast:	n/a	n/a
8	SP1	chr19:36192841-36194093	A549	lung:	n/a	chr19:36193408-36193429 chr19:36193358-36193379 chr19:36193673-36193687 chr19:36193310-36193322 chr19:36193598-36193611
9	POLR2A	chr19:36192862-36194046	GM12892	blood:	n/a	n/a
10	POLR2A	chr19:36192278-36194033	GM12878	blood:	n/a	n/a
11	POLR2A	chr19:36192816-36194277	HepG2	liver:	n/a	n/a
12	FOXA2	chr19:36192543-36193904	A549	lung:	n/a	n/a
13	RUNX3	chr19:36192899-36193982	GM12878	blood:	n/a	n/a
14	POLR2A	chr19:36192541-36194113	GM12878	blood:	n/a	n/a
15	REST	chr19:36192903-36194005	A549	lung:	n/a	chr19:36193210-36193230 chr19:36193466-36193479 chr19:36193170-36193190 chr19:36193210-36193230
16	MXI1	chr19:36192884-36194040	SK-N-SH	brain:	n/a	n/a
17	TCF12	chr19:36192630-36194102	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:36190946..36193857-chr19:36221816..36224169,2	K562	blood:
2	chr19:36192706..36195143-chr19:36207502..36210108,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZBTB32-3	chr19:36192573-36192924	NONHSAT065887

Variant related genes	Relation type
ZBTB32	TF binding region
ENSG00000105663	Chromatin interaction
ENSG00000272333	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10402601	0.89[YRI][hapmap]
rs10402837	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10413852	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[EUR][1000 genomes]
rs12104249	0.86[EUR][1000 genomes]
rs12461285	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12463059	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2234371	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28633929	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs2871921	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[ASN][1000 genomes]
rs34031911	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35209304	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35729071	0.87[CEU][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3848662	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs3848665	0.88[ASN][1000 genomes]
rs56189160	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62109452	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62109998	0.90[EUR][1000 genomes]
rs7249885	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73048504	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8106959	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9304874	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	nsv543995	chr19:36139204-36203592	Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv911630	chr19:36149761-36290977	Enhancers Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	69 gene(s)	inside rSNPs	diseases
4	nsv458566	chr19:36156588-36265508	Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
5	nsv579422	chr19:36156588-36265508	Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
6	nsv911631	chr19:36169285-36290977	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
7	nsv911632	chr19:36174176-36288297	Strong transcription Active TSS Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
8	nsv961286	chr19:36187862-36199437	Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Weak transcription Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv138418	chr19:36190656-36193931	Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12461333	TMEM149	cis	normal skin	skin_eQTL
rs12461333	TMEM149	cis	Brain Pons	GTEx
rs12461333	RN7SL765P	cis	Muscle Skeletal	GTEx
rs12461333	U2AF1L4	Cis_1M	lymphoblastoid	RTeQTL
rs12461333	TMEM149	Cis_1M	lymphoblastoid	RTeQTL
rs12461333	U2AF1L4	cis	Muscle Skeletal	GTEx

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36183000-36193000	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr19:36189600-36193000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr19:36192600-36193000	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
4	chr19:36192600-36193000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
5	chr19:36192600-36193000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr19:36192600-36193000	Enhancers	Placenta	Placenta
7	chr19:36192600-36193000	Enhancers	Fetal Thymus	thymus
8	chr19:36192600-36193600	Active TSS	iPS-15b Cell Line	embryonic stem cell
9	chr19:36192600-36194000	Active TSS	H9 Cell Line	embryonic stem cell
10	chr19:36192600-36194200	Flanking Active TSS	Dnd41	blood
11	chr19:36192800-36193000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
12	chr19:36192800-36193000	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
13	chr19:36192800-36193000	Enhancers	Primary B cells from cord blood	blood
14	chr19:36192800-36193000	Enhancers	Primary T cells from cord blood	blood
15	chr19:36192800-36193000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
16	chr19:36192800-36193000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
17	chr19:36192800-36193000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr19:36192800-36193000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
19	chr19:36192800-36193000	Enhancers	Adipose Nuclei	Adipose
20	chr19:36192800-36193000	Enhancers	Liver	Liver
21	chr19:36192800-36193000	Enhancers	Brain Substantia Nigra	brain
22	chr19:36192800-36193000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
23	chr19:36192800-36193000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
24	chr19:36192800-36193000	Bivalent Enhancer	Fetal Muscle Leg	muscle
25	chr19:36192800-36193000	Enhancers	Pancreas	Pancrea
26	chr19:36192800-36193000	Enhancers	HepG2	liver
27	chr19:36192800-36193000	Active TSS	HMEC	breast
28	chr19:36192800-36193000	Bivalent/Poised TSS	Monocytes-CD14+_RO01746	blood
29	chr19:36192800-36193200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
30	chr19:36192800-36193200	Flanking Active TSS	Primary B cells from peripheral blood	blood
31	chr19:36192800-36193200	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
32	chr19:36192800-36193200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
33	chr19:36192800-36193200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
34	chr19:36192800-36193200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
35	chr19:36192800-36193200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
36	chr19:36192800-36193200	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr19:36192800-36193200	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
38	chr19:36192800-36193200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
39	chr19:36192800-36193200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr19:36192800-36193200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr19:36192800-36193200	Flanking Active TSS	Colonic Mucosa	Colon
42	chr19:36192800-36193400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
43	chr19:36192800-36193600	Active TSS	ES-I3 Cell Line	embryonic stem cell
44	chr19:36192800-36193600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr19:36192800-36193600	Active TSS	HUES48 Cell Line	embryonic stem cell
46	chr19:36192800-36193600	Active TSS	HUES6 Cell Line	embryonic stem cell
47	chr19:36192800-36193600	Active TSS	HUES64 Cell Line	embryonic stem cell
48	chr19:36192800-36193600	Active TSS	iPS-18 Cell Line	embryonic stem cell
49	chr19:36192800-36193600	Active TSS	iPS-20b Cell Line	embryonic stem cell
50	chr19:36192800-36193600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell

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