Variant report

Variant	rs12461285
Chromosome Location	chr19:36193380-36193381
allele	G/T
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	STAT3	chr19:36193087-36193699	GM12878	blood:	n/a	n/a
2	ARID3A	chr19:36193208-36193573	K562	blood:	n/a	n/a
3	CUX1	chr19:36193146-36193760	GM12878	blood:	n/a	n/a
4	EBF1	chr19:36193093-36193899	GM12878	blood:	n/a	n/a
5	KAP1	chr19:36193093-36193806	U2OS	brain:	n/a	n/a
6	MTA3	chr19:36192897-36194080	GM12878	blood:	n/a	n/a
7	POLR2A	chr19:36193001-36194079	GM12878	blood:	n/a	n/a
8	FOS	chr19:36193141-36193712	K562	blood:	n/a	chr19:36193478-36193487 chr19:36193417-36193426 chr19:36193361-36193370 chr19:36193313-36193322
9	RCOR1	chr19:36193150-36193765	HepG2	liver:	n/a	n/a
10	SP1	chr19:36192953-36193990	GM12878	blood:	n/a	chr19:36193408-36193429 chr19:36193358-36193379 chr19:36193673-36193687 chr19:36193310-36193322 chr19:36193598-36193611
11	POLR2A	chr19:36192900-36194052	GM12892	blood:	n/a	n/a
12	THAP1	chr19:36193272-36193447	K562	blood:	n/a	n/a
13	TAF1	chr19:36193035-36193488	H1-hESC	embryonic stem cell:	n/a	n/a
14	SP2	chr19:36193177-36193674	H1-hESC	embryonic stem cell:	n/a	chr19:36193460-36193475 chr19:36193417-36193427 chr19:36193360-36193370
15	PML	chr19:36192844-36193964	GM12878	blood:	n/a	n/a
16	RCOR1	chr19:36193006-36193935	GM12878	blood:	n/a	n/a
17	SP2	chr19:36192992-36193742	HepG2	liver:	n/a	chr19:36193460-36193475 chr19:36193417-36193427 chr19:36193360-36193370
18	CTCF	chr19:36193240-36193390	GM12873	blood:	n/a	n/a
19	E2F6	chr19:36193070-36193864	K562	blood:	n/a	chr19:36193359-36193368 chr19:36193308-36193319 chr19:36193476-36193485
20	POLR2A	chr19:36193119-36194024	H1-neurons	neurons:	n/a	n/a
21	POLR2A	chr19:36193017-36193882	A549	lung:	n/a	n/a
22	SP1	chr19:36193061-36193673	K562	blood:	n/a	chr19:36193408-36193429 chr19:36193358-36193379 chr19:36193310-36193322 chr19:36193598-36193611
23	E2F4	chr19:36193106-36193844	GM12878	blood:	n/a	chr19:36193359-36193368 chr19:36193476-36193485
24	ZNF263	chr19:36193046-36193793	HEK293-T-REx	kidney:	n/a	chr19:36193197-36193218
25	ZEB1	chr19:36193223-36193501	GM12878	blood:	n/a	n/a
26	ZBTB33	chr19:36193107-36193557	A549	lung:	n/a	n/a
27	SP1	chr19:36192975-36193648	H1-hESC	embryonic stem cell:	n/a	chr19:36193408-36193429 chr19:36193358-36193379 chr19:36193310-36193322 chr19:36193598-36193611
28	GABPA	chr19:36193168-36193994	MCF-7	breast:	n/a	n/a
29	HCFC1	chr19:36193347-36193407	K562	blood:	n/a	n/a
30	MXI1	chr19:36193289-36193489	K562	blood:	n/a	n/a
31	JUND	chr19:36192981-36193814	A549	lung:	n/a	chr19:36193478-36193487 chr19:36193417-36193426 chr19:36193361-36193370 chr19:36193313-36193322
32	ELF1	chr19:36193233-36193473	K562	blood:	n/a	n/a
33	BCL3	chr19:36192937-36193932	A549	lung:	n/a	chr19:36193592-36193601 chr19:36193896-36193904 chr19:36193496-36193509
34	MAFF	chr19:36193260-36193793	HepG2	liver:	n/a	chr19:36193681-36193699
35	MAFK	chr19:36193125-36193761	Hela-S3	cervix:	n/a	n/a
36	WRNIP1	chr19:36193082-36193424	GM12878	blood:	n/a	n/a
37	TAF1	chr19:36193220-36193394	PFSK-1	brain:	n/a	n/a
38	TAF1	chr19:36193086-36193911	HepG2	liver:	n/a	n/a
39	NFYA	chr19:36193127-36193729	GM12878	blood:	n/a	chr19:36193357-36193371 chr19:36193476-36193486 chr19:36193474-36193488 chr19:36193418-36193428 chr19:36193357-36193372 chr19:36193474-36193487 chr19:36193357-36193375 chr19:36193474-36193489 chr19:36193357-36193372 chr19:36193418-36193428 chr19:36193474-36193489
40	MAX	chr19:36193064-36193978	GM12878	blood:	n/a	n/a
41	TCF12	chr19:36192972-36193612	A549	lung:	n/a	n/a
42	SP1	chr19:36192879-36194047	A549	lung:	n/a	chr19:36193408-36193429 chr19:36193358-36193379 chr19:36193673-36193687 chr19:36193310-36193322 chr19:36193598-36193611
43	RFX5	chr19:36193091-36193803	GM12878	blood:	n/a	chr19:36193477-36193486 chr19:36193360-36193369 chr19:36193418-36193427
44	PBX3	chr19:36193139-36193889	GM12878	blood:	n/a	chr19:36193477-36193486 chr19:36193769-36193778 chr19:36193360-36193369 chr19:36193418-36193427
45	MAX	chr19:36193094-36193928	MCF-7	breast:	n/a	n/a
46	PAX5	chr19:36193069-36194108	GM12878	blood:	n/a	chr19:36193386-36193404 chr19:36193311-36193329 chr19:36193310-36193329
47	TAF1	chr19:36193084-36193971	PFSK-1	brain:	n/a	n/a
48	NFYB	chr19:36193003-36193880	Hela-S3	cervix:	n/a	chr19:36193357-36193371 chr19:36193476-36193486 chr19:36193417-36193432 chr19:36193474-36193488 chr19:36193418-36193428 chr19:36193357-36193372 chr19:36193354-36193369 chr19:36193474-36193487 chr19:36193474-36193489 chr19:36193357-36193372 chr19:36193418-36193428 chr19:36193474-36193489
49	BCL3	chr19:36192934-36193904	A549	lung:	n/a	chr19:36193592-36193601 chr19:36193896-36193904 chr19:36193496-36193509
50	NFYA	chr19:36193082-36194072	Hela-S3	cervix:	n/a	chr19:36193357-36193371 chr19:36193476-36193486 chr19:36193474-36193488 chr19:36193418-36193428 chr19:36193357-36193372 chr19:36193474-36193487 chr19:36193357-36193375 chr19:36193474-36193489 chr19:36193357-36193372 chr19:36193418-36193428 chr19:36193474-36193489

No.	Distal block	Cell Line	Cell type
1	chr19:36134071..36136376-chr19:36193211..36195269,2	MCF-7	breast:
2	chr19:36193261..36195251-chr19:36208816..36211234,2	K562	blood:
3	chr19:36193001..36195251-chr19:36206737..36211234,4	K562	blood:
4	chr19:36184467..36185236-chr19:36193340..36194279,2	MCF-7	breast:
5	chr19:36190946..36193857-chr19:36221816..36224169,2	K562	blood:
6	chr19:36192706..36195143-chr19:36207502..36210108,2	MCF-7	breast:

Variant related genes	Relation type
ZBTB32	TF binding region
ENSG00000272333	Chromatin interaction
ENSG00000105663	Chromatin interaction
ENSG00000105672	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10402837	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10413852	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12104249	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12461333	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	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2234371	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28633929	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs2871921	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs34031911	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35209304	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35729071	0.88[CEU][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3848662	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3848665	0.90[ASN][1000 genomes]
rs56170803	0.81[ASN][1000 genomes]
rs56189160	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62109452	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62109998	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7249885	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7254601	0.82[JPT][hapmap]
rs73048504	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8106959	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9304874	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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
rs12461285	TMEM149	cis	Brain Pons	GTEx
rs12461285	U2AF1L4	cis	Muscle Skeletal	GTEx
rs12461285	U2AF1L4	Cis_1M	lymphoblastoid	RTeQTL
rs12461285	TMEM149	Cis_1M	lymphoblastoid	RTeQTL
rs12461285	TMEM149	cis	multi-tissue	Pritchard
rs12461285	RN7SL765P	cis	Muscle Skeletal	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36192600-36193600	Active TSS	iPS-15b Cell Line	embryonic stem cell
2	chr19:36192600-36194000	Active TSS	H9 Cell Line	embryonic stem cell
3	chr19:36192600-36194200	Flanking Active TSS	Dnd41	blood
4	chr19:36192800-36193400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
5	chr19:36192800-36193600	Active TSS	ES-I3 Cell Line	embryonic stem cell
6	chr19:36192800-36193600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr19:36192800-36193600	Active TSS	HUES48 Cell Line	embryonic stem cell
8	chr19:36192800-36193600	Active TSS	HUES6 Cell Line	embryonic stem cell
9	chr19:36192800-36193600	Active TSS	HUES64 Cell Line	embryonic stem cell
10	chr19:36192800-36193600	Active TSS	iPS-18 Cell Line	embryonic stem cell
11	chr19:36192800-36193600	Active TSS	iPS-20b Cell Line	embryonic stem cell
12	chr19:36192800-36193600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr19:36192800-36193600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr19:36192800-36193600	Active TSS	Brain Cingulate Gyrus	brain
15	chr19:36192800-36193600	Active TSS	Rectal Mucosa Donor 29	rectum
16	chr19:36192800-36193600	Active TSS	Stomach Smooth Muscle	stomach
17	chr19:36192800-36193600	Active TSS	Hela-S3	cervix
18	chr19:36192800-36193600	Active TSS	K562	blood
19	chr19:36192800-36193800	Active TSS	H1 Cell Line	embryonic stem cell
20	chr19:36192800-36193800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr19:36192800-36193800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr19:36192800-36193800	Active TSS	Brain Angular Gyrus	brain
23	chr19:36192800-36193800	Active TSS	Colon Smooth Muscle	Colon
24	chr19:36192800-36193800	Active TSS	Fetal Brain Female	brain
25	chr19:36192800-36193800	Active TSS	Rectal Smooth Muscle	rectum
26	chr19:36192800-36194000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
27	chr19:36192800-36194000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
28	chr19:36192800-36194000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
29	chr19:36192800-36194000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr19:36192800-36194000	Active TSS	Brain Germinal Matrix	brain
31	chr19:36192800-36194000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
32	chr19:36192800-36194000	Active TSS	Right Atrium	heart
33	chr19:36192800-36194200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr19:36192800-36194200	Active TSS	Brain Anterior Caudate	brain
35	chr19:36192800-36194200	Active TSS	Brain Hippocampus Middle	brain
36	chr19:36192800-36194200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
37	chr19:36192800-36194200	Active TSS	Right Ventricle	heart
38	chr19:36192800-36194200	Active TSS	A549	lung
39	chr19:36192800-36194200	Active TSS	GM12878-XiMat	blood
40	chr19:36192800-36194400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr19:36193000-36193400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
42	chr19:36193000-36193400	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
43	chr19:36193000-36193400	Flanking Active TSS	Fetal Thymus	thymus
44	chr19:36193000-36193400	Enhancers	Sigmoid Colon	Sigmoid Colon
45	chr19:36193000-36193600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr19:36193000-36193600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
47	chr19:36193000-36193600	Active TSS	Primary T cells from cord blood	blood
48	chr19:36193000-36193600	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
49	chr19:36193000-36193600	Active TSS	Primary T killer memory cells from peripheral blood	blood
50	chr19:36193000-36193600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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