Variant report

Variant	rs1552039
Chromosome Location	chr12:75905994-75905995
allele	A/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	REST	chr12:75904781-75905994	HL-60	blood:	n/a	n/a
2	MAX	chr12:75905025-75905996	A549	lung:	n/a	n/a
3	ZNF143	chr12:75904897-75906051	K562	blood:	n/a	chr12:75905612-75905621 chr12:75905610-75905619 chr12:75905603-75905621
4	GABPA	chr12:75904655-75906158	A549	lung:	n/a	n/a
5	POLR2A	chr12:75903564-75906140	GM12891	blood:	n/a	n/a
6	CBX3	chr12:75905036-75906064	HCT-116	colon:	n/a	n/a
7	NRF1	chr12:75904368-75906277	SK-N-SH	brain:	n/a	n/a
8	HCFC1	chr12:75905041-75906121	K562	blood:	n/a	n/a
9	CBX3	chr12:75904921-75905995	HCT-116	colon:	n/a	n/a
10	ETS1	chr12:75904976-75906084	A549	lung:	n/a	chr12:75905386-75905395 chr12:75905609-75905622 chr12:75905386-75905395 chr12:75905386-75905395 chr12:75905386-75905395 chr12:75905386-75905395 chr12:75905384-75905394 chr12:75905386-75905395
11	MAX	chr12:75904917-75905996	A549	lung:	n/a	n/a
12	SIX5	chr12:75904713-75906221	A549	lung:	n/a	chr12:75905609-75905623 chr12:75905612-75905621 chr12:75905610-75905619
13	MEF2A	chr12:75905181-75906006	GM12878	blood:	n/a	chr12:75905902-75905916 chr12:75905900-75905921
14	E2F6	chr12:75905008-75906110	A549	lung:	n/a	n/a
15	KAP1	chr12:75905163-75906019	K562	blood:	n/a	n/a
16	POLR2A	chr12:75904953-75906195	NB4	blood:	n/a	n/a
17	TCF12	chr12:75904691-75906203	A549	lung:	n/a	chr12:75905104-75905111
18	POLR2A	chr12:75904896-75906036	Hela-S3	cervix:	n/a	n/a
19	CBX3	chr12:75904943-75906015	K562	blood:	n/a	n/a
20	EP300	chr12:75905976-75906173	GM12878	blood:	n/a	n/a
21	GATA1	chr12:75904584-75906044	PBDE	blood:	n/a	chr12:75905151-75905167 chr12:75905155-75905164
22	HCFC1	chr12:75904311-75906508	Hela-S3	cervix:	n/a	n/a
23	JUND	chr12:75904837-75906006	K562	blood:	n/a	n/a
24	GABPA	chr12:75904569-75906019	A549	lung:	n/a	n/a
25	MAX	chr12:75904874-75906048	HCT-116	colon:	n/a	n/a
26	GABPA	chr12:75904424-75906167	MCF-7	breast:	n/a	n/a
27	MAX	chr12:75904981-75905998	MCF-7	breast:	n/a	n/a
28	IRF1	chr12:75905002-75906001	K562	blood:	n/a	chr12:75905403-75905414 chr12:75905400-75905414
29	MYC	chr12:75904664-75906130	K562	blood:	n/a	n/a
30	TBL1XR1	chr12:75905014-75906062	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:75905251..75907126-chr12:76425328..76426938,2	MCF-7	breast:

Variant related genes	Relation type
KRR1	TF binding region
ENSG00000139289	Chromatin interaction
ENSG00000257839	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10506667	1.00[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap];0.95[YRI][hapmap]
rs11180480	0.83[JPT][hapmap]
rs11180552	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11180560	0.95[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11355	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1147995	0.92[CHB][hapmap];0.92[JPT][hapmap]
rs11540407	0.95[CEU][hapmap];0.93[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.90[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11609405	0.80[ASN][1000 genomes]
rs11610328	0.95[CEU][hapmap];0.92[CHB][hapmap];0.81[GIH][hapmap];0.92[JPT][hapmap];0.81[LWK][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11611121	0.95[CEU][hapmap];0.92[CHB][hapmap];0.91[JPT][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11611609	1.00[CEU][hapmap];0.92[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.91[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11612665	0.83[ASN][1000 genomes]
rs12425122	0.84[ASN][1000 genomes]
rs12811160	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12812559	1.00[CEU][hapmap];0.92[CHB][hapmap];0.91[JPT][hapmap];0.94[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12815116	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12819511	1.00[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12822366	0.83[ASN][1000 genomes]
rs12822493	0.92[CHB][hapmap];0.81[ASN][1000 genomes]
rs12822505	0.83[ASN][1000 genomes]
rs12826635	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12827668	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12827986	0.81[ASN][1000 genomes]
rs1501634	1.00[CEU][hapmap];0.85[CHB][hapmap];0.92[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs15513	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1604381	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17217158	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap];0.89[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17218895	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17818307	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1824981	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2054517	0.92[CHB][hapmap];0.92[JPT][hapmap];0.81[ASN][1000 genomes]
rs2070162	0.84[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.95[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2202105	0.83[ASN][1000 genomes]
rs2279244	0.82[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.95[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2306391	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.91[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34508642	0.83[ASN][1000 genomes]
rs35124104	0.84[ASN][1000 genomes]
rs35244242	0.83[ASN][1000 genomes]
rs35351465	0.83[ASN][1000 genomes]
rs35619460	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3741495	0.84[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3809118	0.95[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3809121	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4420306	0.83[ASN][1000 genomes]
rs4760596	0.83[ASN][1000 genomes]
rs56049502	0.81[ASN][1000 genomes]
rs61933361	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61933362	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61933387	0.81[ASN][1000 genomes]
rs7961005	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv492067	chr12:75415458-76077537	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv1036987	chr12:75415532-76101559	Weak transcription Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv899313	chr12:75715330-76057811	Weak transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	nsv1040583	chr12:75742802-76360276	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv428592	chr12:75766619-75936721	Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	nsv948653	chr12:75773464-76220618	Active TSS Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
7	nsv470305	chr12:75896688-75987360	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs1552039	GLIPR1L2	cis	cerebellum	SCAN
rs1552039	GLIPR1	cis	uninvolved skin	skin_eQTL
rs1552039	KRR1	cis	parietal	SCAN
rs1552039	GLIPR1	Cis_1M	lymphoblastoid	RTeQTL
rs1552039	PTPRB	cis	parietal	SCAN
rs1552039	GLIPR1	cis	normal skin	skin_eQTL
rs1552039	GLIPR1	cis	lesional skin	skin_eQTL
rs1552039	GLIPR1	cis	lymphoblastoid	seeQTL
rs1552039	KRR1	cis	Muscle Skeletal	GTEx
rs1552039	LRRN1	trans	cerebellum	SCAN
rs1552039	KRR1	cis	cerebellum	SCAN
rs1552039	GLIPR1	cis	parietal	SCAN
rs1552039	GLIPR1L2	cis	parietal	SCAN

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:75903200-75906000	Active TSS	Breast Myoepithelial Primary Cells	Breast
2	chr12:75903400-75906000	Active TSS	HUES6 Cell Line	embryonic stem cell
3	chr12:75903800-75906000	Active TSS	iPS-18 Cell Line	embryonic stem cell
4	chr12:75903800-75906200	Active TSS	A549	lung
5	chr12:75904000-75906000	Active TSS	iPS-15b Cell Line	embryonic stem cell
6	chr12:75904000-75906000	Active TSS	Psoas Muscle	Psoas
7	chr12:75904200-75906000	Active TSS	ES-I3 Cell Line	embryonic stem cell
8	chr12:75904200-75906000	Active TSS	HUES48 Cell Line	embryonic stem cell
9	chr12:75904200-75906000	Active TSS	HUES64 Cell Line	embryonic stem cell
10	chr12:75904200-75906000	Active TSS	iPS-20b Cell Line	embryonic stem cell
11	chr12:75904200-75906000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr12:75904200-75906000	Active TSS	Fetal Thymus	thymus
13	chr12:75904200-75906000	Active TSS	Right Atrium	heart
14	chr12:75904200-75906000	Active TSS	NH-A	brain
15	chr12:75904400-75906000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr12:75904400-75906000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr12:75904400-75906000	Active TSS	Primary hematopoietic stem cells short term culture	blood
18	chr12:75904400-75906000	Active TSS	Primary T helper cells PMA-I stimulated	--
19	chr12:75904400-75906000	Active TSS	Muscle Satellite Cultured Cells	--
20	chr12:75904400-75906000	Active TSS	Fetal Muscle Leg	muscle
21	chr12:75904400-75906000	Active TSS	NHLF	lung
22	chr12:75904600-75906000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
23	chr12:75904600-75906000	Active TSS	Brain Angular Gyrus	brain
24	chr12:75904600-75906000	Active TSS	Brain Germinal Matrix	brain
25	chr12:75904600-75906000	Active TSS	Fetal Kidney	kidney
26	chr12:75904600-75906000	Active TSS	Rectal Mucosa Donor 29	rectum
27	chr12:75904600-75906000	Active TSS	Skeletal Muscle Male	skeletal muscle
28	chr12:75904600-75906000	Active TSS	Thymus	Thymus
29	chr12:75904600-75906000	Active TSS	Osteobl	bone
30	chr12:75904800-75906000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr12:75904800-75906000	Active TSS	Cortex derived primary cultured neurospheres	brain
32	chr12:75904800-75906000	Active TSS	Brain Anterior Caudate	brain
33	chr12:75904800-75906000	Active TSS	Brain Cingulate Gyrus	brain
34	chr12:75904800-75906000	Active TSS	Brain Hippocampus Middle	brain
35	chr12:75904800-75906000	Active TSS	Colonic Mucosa	Colon
36	chr12:75904800-75906000	Active TSS	Fetal Adrenal Gland	Adrenal Gland
37	chr12:75904800-75906000	Active TSS	Fetal Brain Female	brain
38	chr12:75904800-75906000	Active TSS	Pancreatic Islets	Pancreatic Islet
39	chr12:75904800-75906000	Active TSS	Fetal Stomach	stomach
40	chr12:75904800-75906000	Active TSS	Rectal Smooth Muscle	rectum
41	chr12:75904800-75906000	Active TSS	Stomach Smooth Muscle	stomach
42	chr12:75905000-75906000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr12:75905000-75906000	Active TSS	Primary T cells from cord blood	blood
44	chr12:75905000-75906000	Active TSS	Liver	Liver
45	chr12:75905000-75906000	Active TSS	Brain Inferior Temporal Lobe	brain
46	chr12:75905000-75906000	Active TSS	Skeletal Muscle Female	skeletal muscle
47	chr12:75905200-75906000	Active TSS	Primary B cells from cord blood	blood
48	chr12:75905200-75906000	Active TSS	Primary T cells fromperipheralblood	blood
49	chr12:75905200-75906000	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr12:75905400-75906000	Flanking Active TSS	Dnd41	blood

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