Variant report

Variant	rs2242435
Chromosome Location	chr12:75874913-75874914
allele	C/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	MYC	chr12:75874217-75874992	MCF10A-Er-Src	breast:	n/a	n/a
2	WRNIP1	chr12:75874413-75875765	GM12878	blood:	n/a	n/a
3	POLR2A	chr12:75873773-75875900	GM18505	blood:	n/a	n/a
4	RCOR1	chr12:75873963-75875530	GM12878	blood:	n/a	n/a
5	POLR2A	chr12:75874369-75875903	NB4	blood:	n/a	n/a
6	PML	chr12:75873845-75875194	GM12878	blood:	n/a	n/a
7	POLR2A	chr12:75873454-75877588	MCF10A-Er-Src	breast:	n/a	n/a
8	POLR2A	chr12:75874430-75875879	GM12878	blood:	n/a	n/a
9	MAX	chr12:75874253-75875738	NB4	blood:	n/a	n/a
10	MAX	chr12:75874224-75875140	A549	lung:	n/a	n/a
11	TBP	chr12:75873952-75876024	GM12878	blood:	n/a	n/a
12	POLR2A	chr12:75874328-75875058	ProgFib	skin:	n/a	n/a
13	SPI1	chr12:75874888-75875190	K562	blood:	n/a	chr12:75875056-75875065 chr12:75875055-75875068
14	CREB1	chr12:75873912-75874981	GM12878	blood:	n/a	n/a
15	BCLAF1	chr12:75873883-75875174	GM12878	blood:	n/a	chr12:75875055-75875064
16	POLR2A	chr12:75873661-75875927	GM12878	blood:	n/a	n/a
17	SPI1	chr12:75874395-75875445	GM12878	blood:	n/a	chr12:75875056-75875065 chr12:75875055-75875068
18	MAX	chr12:75874326-75874982	A549	lung:	n/a	n/a
19	RUNX3	chr12:75873742-75875506	GM12878	blood:	n/a	n/a
20	POLR2A	chr12:75874163-75875374	HUVEC	blood vessel:	n/a	n/a
21	EP300	chr12:75873879-75875869	GM12878	blood:	n/a	chr12:75875056-75875065 chr12:75874377-75874386 chr12:75875599-75875609 chr12:75875083-75875097
22	POLR2A	chr12:75874335-75875181	GM19193	blood:	n/a	n/a
23	POLR2A	chr12:75874343-75875146	GM12892	blood:	n/a	n/a
24	SPI1	chr12:75874843-75875234	GM12878	blood:	n/a	chr12:75875056-75875065 chr12:75875055-75875068
25	POLR2A	chr12:75874305-75875875	GM12878	blood:	n/a	n/a
26	MTA3	chr12:75873464-75876093	GM12878	blood:	n/a	n/a
27	POLR2A	chr12:75874371-75875225	HUVEC	blood vessel:	n/a	n/a
28	SPI1	chr12:75874911-75875309	HL-60	blood:	n/a	chr12:75875056-75875065 chr12:75875055-75875068
29	CUX1	chr12:75874558-75875197	GM12878	blood:	n/a	n/a
30	CCNT2	chr12:75874519-75875022	K562	blood:	n/a	n/a
31	MYC	chr12:75874284-75875142	MCF10A-Er-Src	breast:	n/a	n/a
32	MYC	chr12:75874250-75875428	NB4	blood:	n/a	n/a
33	POLR2A	chr12:75874253-75875040	GM12892	blood:	n/a	n/a
34	SPI1	chr12:75874833-75875240	GM12891	blood:	n/a	chr12:75875056-75875065 chr12:75875055-75875068
35	SPI1	chr12:75874867-75875290	GM12891	blood:	n/a	chr12:75875056-75875065 chr12:75875055-75875068
36	POLR2A	chr12:75874286-75875117	GM12891	blood:	n/a	n/a
37	CHD1	chr12:75873981-75875286	GM12878	blood:	n/a	n/a
38	SMC3	chr12:75874160-75875240	GM12878	blood:	n/a	n/a
39	RUNX3	chr12:75874837-75875480	GM12878	blood:	n/a	n/a
40	POLR2A	chr12:75874116-75875009	U87	brain:	n/a	n/a
41	MXI1	chr12:75873982-75875800	GM12878	blood:	n/a	n/a
42	POLR2A	chr12:75873874-75875313	GM18951	blood:	n/a	n/a
43	NFIC	chr12:75873747-75875197	GM12878	blood:	n/a	n/a
44	POLR2A	chr12:75873958-75875991	GM19099	blood:	n/a	n/a
45	POLR2A	chr12:75873593-75876813	IMR90	lung:	n/a	n/a
46	SPI1	chr12:75874284-75875448	HL-60	blood:	n/a	chr12:75875056-75875065 chr12:75875055-75875068
47	POLR2A	chr12:75873977-75875083	GM15510	blood:	n/a	n/a
48	MAFK	chr12:75874289-75875353	IMR90	lung:	n/a	n/a
49	PBX3	chr12:75874287-75875115	SK-N-SH	brain:	n/a	n/a
50	POLR2A	chr12:75874306-75874968	GM12891	blood:	n/a	n/a

Variant related genes	Relation type
GLIPR1	TF binding region

Extended variants
information (count: 99 )
Associated
traits (count: 27 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs10506668	0.89[CEU][hapmap];0.86[CHB][hapmap];0.87[CHD][hapmap];0.90[MEX][hapmap];0.80[TSI][hapmap]
rs1051446	0.89[CEU][hapmap];0.88[GIH][hapmap];0.80[TSI][hapmap]
rs10785187	0.89[CEU][hapmap];0.86[CHB][hapmap]
rs10879902	0.86[JPT][hapmap]
rs10879903	0.86[JPT][hapmap]
rs10879905	0.89[CEU][hapmap];0.86[CHB][hapmap]
rs10879907	0.89[CEU][hapmap]
rs10879916	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10879918	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10879919	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10879922	0.89[CEU][hapmap];0.93[GIH][hapmap];0.90[MEX][hapmap];0.82[TSI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10879923	0.89[CEU][hapmap];0.83[EUR][1000 genomes]
rs11180460	0.86[JPT][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap]
rs11180465	0.80[MEX][hapmap]
rs11180474	0.86[JPT][hapmap]
rs11180483	0.89[CEU][hapmap];0.86[CHB][hapmap];0.87[CHD][hapmap];0.90[MEX][hapmap];0.80[TSI][hapmap]
rs11180512	0.89[CEU][hapmap];0.86[CHB][hapmap];0.80[AMR][1000 genomes]
rs11180524	0.80[AMR][1000 genomes]
rs11180526	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11180527	0.83[AMR][1000 genomes]
rs11180528	0.83[AMR][1000 genomes]
rs11180533	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11180535	0.83[AMR][1000 genomes]
rs11180536	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11180537	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11180538	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11180540	0.89[CEU][hapmap];0.86[CHB][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];0.95[MEX][hapmap];0.82[TSI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11180546	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11180547	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11180548	0.89[CEU][hapmap];0.82[CHB][hapmap];0.82[CHD][hapmap];0.90[GIH][hapmap];0.90[MEX][hapmap];0.82[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11831200	0.86[JPT][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap]
rs11831340	0.80[AMR][1000 genomes]
rs11837697	0.86[JPT][hapmap];0.95[MEX][hapmap];0.83[TSI][hapmap]
rs12146845	0.83[AMR][1000 genomes]
rs12146849	0.82[AMR][1000 genomes]
rs12369556	0.89[CEU][hapmap];0.86[CHB][hapmap];0.87[CHD][hapmap];0.90[MEX][hapmap];0.80[TSI][hapmap]
rs12371293	0.89[CEU][hapmap];0.86[CHB][hapmap]
rs12422952	0.89[CEU][hapmap];0.82[CHB][hapmap];0.83[EUR][1000 genomes]
rs12579161	0.80[AMR][1000 genomes]
rs12581394	0.80[MEX][hapmap]
rs12581416	0.86[JPT][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap]
rs12582825	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17115087	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17115098	0.89[CEU][hapmap];0.86[CHB][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1875471	0.88[CEU][hapmap];0.86[CHB][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1909971	0.81[EUR][1000 genomes]
rs1909972	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1909973	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1909979	0.89[CEU][hapmap];0.86[CHB][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];0.95[MEX][hapmap];0.82[TSI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2292009	0.89[CEU][hapmap];0.86[CHB][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2292010	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3087687	0.86[JPT][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap]
rs3741496	0.89[CEU][hapmap];0.90[GIH][hapmap];0.85[MEX][hapmap];0.82[TSI][hapmap]
rs3759089	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3759090	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4394867	0.89[CEU][hapmap];0.86[CHB][hapmap];0.87[CHD][hapmap];0.90[MEX][hapmap];0.80[TSI][hapmap]
rs4409878	0.89[CEU][hapmap];0.86[CHB][hapmap]
rs4415811	0.89[CEU][hapmap];0.86[CHB][hapmap]
rs4565940	0.89[CEU][hapmap];0.86[CHB][hapmap];0.87[CHD][hapmap];0.90[MEX][hapmap];0.80[TSI][hapmap]
rs4623941	0.95[MEX][hapmap]
rs4882616	0.86[JPT][hapmap]
rs4882618	0.89[CEU][hapmap];0.86[CHB][hapmap];0.87[CHD][hapmap];0.95[MEX][hapmap];0.80[TSI][hapmap]
rs4882628	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4882629	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4882687	0.90[MEX][hapmap]
rs56829278	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs57613088	0.83[AMR][1000 genomes]
rs58018505	0.80[AMR][1000 genomes]
rs59282813	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs67705855	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7133490	0.80[AMR][1000 genomes]
rs7134260	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7135164	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7135208	0.80[AMR][1000 genomes]
rs7296131	0.80[AMR][1000 genomes]
rs7298343	0.86[JPT][hapmap];0.89[MEX][hapmap];0.84[TSI][hapmap]
rs7299877	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs7307352	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7315091	0.80[AMR][1000 genomes]
rs7486473	0.80[AMR][1000 genomes]
rs7488050	0.83[AMR][1000 genomes]
rs7957713	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7963723	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7963834	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7963977	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7964070	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7966268	0.89[CEU][hapmap]
rs7966763	0.84[CEU][hapmap];0.86[CHB][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7967014	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7969930	0.89[CEU][hapmap];0.86[CHB][hapmap];0.87[CHD][hapmap];0.90[GIH][hapmap];0.95[MEX][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7974011	0.85[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.95[MEX][hapmap];0.82[TSI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7975661	0.90[MEX][hapmap]
rs7978312	0.95[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 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

mRNA abundance (count:27)

SNP	Gene	Cis/trans	Tissue	Source
rs2242435	KRR1	cis	cerebellum	SCAN
rs2242435	GLIPR1	cis	Whole Blood	GTEx
rs2242435	RP11-585P4.5	cis	Artery Tibial	GTEx
rs2242435	GLIPR1L2	cis	Esophagus Muscularis	GTEx
rs2242435	GLIPR1L2	cis	Heart Left Ventricle	GTEx
rs2242435	RP11-585P4.5	cis	Thyroid	GTEx
rs2242435	GLIPR1L2	cis	Artery Aorta	GTEx
rs2242435	GLIPR1L2	cis	cerebellum	SCAN
rs2242435	GLIPR1L2	cis	Esophagus Mucosa	GTEx
rs2242435	GLIPR1L2	cis	Stomach	GTEx
rs2242435	GLIPR1	cis	parietal	SCAN
rs2242435	GLIPR1	cis	cerebellum	SCAN
rs2242435	GLIPR1L2	cis	Muscle Skeletal	GTEx
rs2242435	GLIPR1L2	cis	lung	GTEx
rs2242435	GLIPR1L2	cis	Artery Tibial	GTEx
rs2242435	RP11-585P4.5	cis	Muscle Skeletal	GTEx
rs2242435	KRR1	cis	parietal	SCAN
rs2242435	GLIPR1L2	cis	Thyroid	GTEx
rs2242435	GLIPR1L2	cis	Adipose Subcutaneous	GTEx
rs2242435	GLIPR1L2	cis	Nerve Tibial	GTEx
rs2242435	GLIPR1L2	cis	parietal	SCAN
rs2242435	RP11-585P4.5	cis	Nerve Tibial	GTEx
rs2242435	RAET1G	trans	cerebellum	SCAN
rs2242435	RP11-585P4.5	cis	Adipose Subcutaneous	GTEx
rs2242435	GLIPR1L2	cis	Skin Sun Exposed Lower leg	GTEx
rs2242435	GLIPR1L1	cis	multi-tissue	Pritchard
rs2242435	GLIPR1L1	cis	lymphoblastoid	seeQTL

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:75868400-75875600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr12:75873400-75878800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr12:75873600-75875000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
4	chr12:75873600-75875000	Active TSS	Skeletal Muscle Male	skeletal muscle
5	chr12:75873600-75875000	Active TSS	A549	lung
6	chr12:75873600-75875400	Active TSS	Stomach Smooth Muscle	stomach
7	chr12:75873600-75875600	Active TSS	Brain Inferior Temporal Lobe	brain
8	chr12:75873600-75877000	Active TSS	Duodenum Smooth Muscle	Duodenum
9	chr12:75873600-75878200	Active TSS	Aorta	Aorta
10	chr12:75873600-75878200	Flanking Active TSS	Dnd41	blood
11	chr12:75873800-75875200	Active TSS	Pancreatic Islets	Pancreatic Islet
12	chr12:75873800-75875200	Active TSS	HSMMtube	muscle
13	chr12:75873800-75875400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr12:75873800-75875400	Active TSS	Duodenum Mucosa	Duodenum
15	chr12:75873800-75875600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr12:75873800-75875600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr12:75873800-75875600	Active TSS	Brain Cingulate Gyrus	brain
18	chr12:75873800-75875600	Weak transcription	Lung	lung
19	chr12:75873800-75875600	Active TSS	Ovary	ovary
20	chr12:75873800-75875800	Active TSS	Brain Angular Gyrus	brain
21	chr12:75873800-75876000	Active TSS	Osteobl	bone
22	chr12:75873800-75876200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr12:75873800-75876200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr12:75873800-75876200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr12:75873800-75876200	Active TSS	NHLF	lung
26	chr12:75873800-75876400	Active TSS	Psoas Muscle	Psoas
27	chr12:75873800-75876600	Active TSS	Breast Myoepithelial Primary Cells	Breast
28	chr12:75873800-75876800	Active TSS	Adipose Nuclei	Adipose
29	chr12:75873800-75878200	Flanking Active TSS	Primary hematopoietic stem cells	blood
30	chr12:75873800-75879000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr12:75874000-75875000	Active TSS	Stomach Mucosa	stomach
32	chr12:75874000-75875200	Active TSS	Primary T killer memory cells from peripheral blood	blood
33	chr12:75874000-75875200	Enhancers	Cortex derived primary cultured neurospheres	brain
34	chr12:75874000-75875400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr12:75874000-75875400	Active TSS	Primary T helper naive cells from peripheral blood	blood
36	chr12:75874000-75875400	Active TSS	Fetal Kidney	kidney
37	chr12:75874000-75875600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr12:75874000-75875600	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
39	chr12:75874000-75875600	Active TSS	Colonic Mucosa	Colon
40	chr12:75874000-75875600	Active TSS	Fetal Lung	lung
41	chr12:75874000-75875600	Active TSS	Left Ventricle	heart
42	chr12:75874000-75875600	Active TSS	Right Ventricle	heart
43	chr12:75874000-75875600	Active TSS	NHDF-Ad	bronchial
44	chr12:75874000-75875800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
45	chr12:75874000-75875800	Active TSS	Fetal Adrenal Gland	Adrenal Gland
46	chr12:75874000-75875800	Active TSS	Fetal Muscle Trunk	muscle
47	chr12:75874000-75875800	Active TSS	HMEC	breast
48	chr12:75874000-75876000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr12:75874000-75876000	Active TSS	GM12878-XiMat	blood
50	chr12:75874000-75876000	Active TSS	HSMM	muscle

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