Variant report

Variant	rs7513803
Chromosome Location	chr1:246932350-246932351
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	RCOR1	chr1:246932043-246933203	IMR90	lung:	n/a	n/a

Variant related genes	Relation type
ENSG00000260855	TF binding region

Extended variants
information (count: 55 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10127783	0.91[TSI][hapmap];0.86[EUR][1000 genomes]
rs10159002	0.82[CEU][hapmap];0.86[EUR][1000 genomes]
rs10802442	0.86[EUR][1000 genomes]
rs10924820	0.82[CEU][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes]
rs10924823	0.82[CEU][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes]
rs10924824	0.82[CEU][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes]
rs12049149	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12058428	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12080111	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12085823	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12090470	0.85[EUR][1000 genomes]
rs12135184	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12144408	0.86[EUR][1000 genomes]
rs34649985	0.86[EUR][1000 genomes]
rs34989088	0.85[EUR][1000 genomes]
rs3795462	0.88[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3795463	0.86[EUR][1000 genomes]
rs3795465	0.92[CEU][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.96[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3935011	0.85[CEU][hapmap];0.82[CHB][hapmap];0.88[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4130316	0.85[EUR][1000 genomes]
rs4244627	0.82[CEU][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes]
rs4244628	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4244630	0.85[EUR][1000 genomes]
rs4926441	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4926448	0.83[ASW][hapmap];0.85[CEU][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4926451	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4926453	1.00[CEU][hapmap];0.87[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.82[MKK][hapmap];0.96[TSI][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4926454	0.86[EUR][1000 genomes]
rs4926455	0.85[EUR][1000 genomes]
rs4926457	0.86[EUR][1000 genomes]
rs60779884	0.80[ASN][1000 genomes]
rs6426328	0.81[JPT][hapmap];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6426331	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6426332	0.87[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6426334	1.00[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6664091	0.92[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6664883	0.82[CEU][hapmap];0.86[EUR][1000 genomes]
rs6686584	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7537149	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7549965	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7556120	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9426267	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949571	chr1:246688635-247240863	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv873421	chr1:246818634-247044692	Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	esv2762192	chr1:246823857-247069232	Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv1006271	chr1:246832606-247276182	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
5	nsv535416	chr1:246832606-247276182	Strong transcription ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
6	nsv430413	chr1:246845971-246975015	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
7	nsv873422	chr1:246854862-247002638	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
8	nsv1011346	chr1:246868799-247133898	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
9	nsv1006262	chr1:246892826-246964775	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
10	nsv523531	chr1:246893948-246967899	Enhancers Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
11	nsv999756	chr1:246894542-246969660	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
12	nsv1009436	chr1:246910373-246965832	Bivalent/Poised TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
13	nsv873423	chr1:246923861-246978504	Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs7513803	OR2M2	cis	cerebellum	SCAN
rs7513803	SCCPDH	cis	lymphoblastoid	seeQTL
rs7513803	RGS7	cis	cerebellum	SCAN
rs7513803	EXO1	cis	parietal	SCAN
rs7513803	ZNF669	cis	parietal	SCAN
rs7513803	OR14I1	cis	cerebellum	SCAN
rs7513803	SMYD3	cis	cerebellum	SCAN

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:246888400-246946400	Weak transcription	Small Intestine	intestine
2	chr1:246888600-246945600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr1:246895000-246942200	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr1:246895400-246938600	Weak transcription	Fetal Heart	heart
5	chr1:246902800-246952800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:246904600-246942800	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr1:246905000-246945800	Weak transcription	Psoas Muscle	Psoas
8	chr1:246912800-246933200	Weak transcription	K562	blood
9	chr1:246917600-246936000	Weak transcription	Primary B cells from peripheral blood	blood
10	chr1:246920800-246944200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr1:246921200-246943200	Strong transcription	Dnd41	blood
12	chr1:246921600-246945800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr1:246922000-246936400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr1:246922200-246932800	Strong transcription	HepG2	liver
15	chr1:246922200-246933000	Strong transcription	Fetal Intestine Large	intestine
16	chr1:246922200-246934400	Strong transcription	Placenta	Placenta
17	chr1:246922200-246936000	Strong transcription	Primary neutrophils fromperipheralblood	blood
18	chr1:246922200-246936000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr1:246922200-246936200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr1:246922200-246937000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr1:246922200-246944600	Strong transcription	Fetal Muscle Trunk	muscle
22	chr1:246922600-246936400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
23	chr1:246923000-246933000	Strong transcription	Primary T cells from cord blood	blood
24	chr1:246923000-246936200	Strong transcription	Primary hematopoietic stem cells	blood
25	chr1:246923200-246945000	Strong transcription	Fetal Muscle Leg	muscle
26	chr1:246923400-246932600	Strong transcription	Skeletal Muscle Male	skeletal muscle
27	chr1:246923600-246933200	Strong transcription	Brain Hippocampus Middle	brain
28	chr1:246924000-246941200	Strong transcription	Primary monocytes fromperipheralblood	blood
29	chr1:246924000-246944200	Strong transcription	Monocytes-CD14+_RO01746	blood
30	chr1:246924400-246934600	Weak transcription	Fetal Brain Male	brain
31	chr1:246924400-246939200	Weak transcription	Colonic Mucosa	Colon
32	chr1:246924400-246945800	Weak transcription	Primary B cells from cord blood	blood
33	chr1:246925200-246952200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr1:246925400-246936600	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr1:246926400-246939200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr1:246927600-246932400	Weak transcription	Rectal Smooth Muscle	rectum
37	chr1:246928200-246933600	Weak transcription	Fetal Kidney	kidney
38	chr1:246928200-246934600	Weak transcription	A549	lung
39	chr1:246928400-246932600	Strong transcription	Left Ventricle	heart
40	chr1:246928600-246937000	Strong transcription	Fetal Stomach	stomach
41	chr1:246928800-246934000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr1:246928800-246944800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr1:246929200-246932400	Strong transcription	Stomach Smooth Muscle	stomach
44	chr1:246929200-246932800	Strong transcription	Brain Cingulate Gyrus	brain
45	chr1:246929200-246932800	Strong transcription	Rectal Mucosa Donor 29	rectum
46	chr1:246929200-246936800	Strong transcription	Fetal Brain Female	brain
47	chr1:246929400-246932400	Weak transcription	HSMM	muscle
48	chr1:246929400-246932800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr1:246929400-246932800	Strong transcription	Cortex derived primary cultured neurospheres	brain
50	chr1:246929400-246932800	Strong transcription	Duodenum Mucosa	Duodenum

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