Variant report

Variant	rs6823184
Chromosome Location	chr4:47839013-47839014
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:47706419..47708274-chr4:47838366..47839313,9	MCF-7	breast:
2	chr4:47688063..47688915-chr4:47838342..47839484,4	MCF-7	breast:
3	chr4:47706456..47708112-chr4:47838146..47839411,13	MCF-7	breast:

Extended variants
information (count: 80 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10002500	0.91[YRI][hapmap]
rs10008818	0.85[CEU][hapmap]
rs10025104	0.80[JPT][hapmap]
rs10028155	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10030927	0.81[JPT][hapmap]
rs10049713	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1012844	0.85[CEU][hapmap]
rs1062858	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10938499	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10938500	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10938504	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10938505	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10938506	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12186152	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12504018	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12506632	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12507439	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12510002	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12641871	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12651301	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1371729	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.95[YRI][hapmap];0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1371731	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1440221	0.84[EUR][1000 genomes]
rs1440227	0.81[JPT][hapmap]
rs1440228	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16860663	0.84[EUR][1000 genomes]
rs17463666	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17573709	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1822030	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1866689	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1984713	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2033893	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2053404	0.80[JPT][hapmap]
rs2289433	0.80[JPT][hapmap]
rs2289435	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2352470	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2661513	0.95[YRI][hapmap]
rs28395298	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28412313	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28460483	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28573115	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28583602	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28636596	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3113881	0.87[YRI][hapmap]
rs321623	0.82[YRI][hapmap]
rs4529019	0.81[JPT][hapmap]
rs4565052	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4695280	0.82[EUR][1000 genomes]
rs4695303	0.80[JPT][hapmap]
rs4695306	0.80[JPT][hapmap]
rs56001837	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6414687	0.80[JPT][hapmap]
rs6447586	0.81[JPT][hapmap]
rs6447587	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6447589	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6447593	0.81[JPT][hapmap]
rs6811177	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6818556	0.80[JPT][hapmap]
rs6823698	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6833758	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6844286	0.81[JPT][hapmap]
rs6858440	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8180146	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9291317	0.80[JPT][hapmap]
rs978094	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9994561	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9995122	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.95[YRI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9997555	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1008515	chr4:47488431-47906835	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv948568	chr4:47488431-47907524	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv1004939	chr4:47488573-47901460	Bivalent Enhancer Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv537080	chr4:47488573-47901460	Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv997471	chr4:47489412-47895223	Weak transcription Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
6	nsv998892	chr4:47493552-47863354	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
7	nsv537081	chr4:47493552-47863354	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
8	nsv1000337	chr4:47493907-47902019	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking 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 miRNA target site	10 gene(s)	inside rSNPs	diseases
9	nsv594118	chr4:47560386-47917730	Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
10	nsv829924	chr4:47670905-47866665	Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv4328	chr4:47816467-47862253	Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	esv3447039	chr4:47822266-48285222	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs6823184	CNGA1	cis	Muscle Skeletal	GTEx
rs6823184	CNGA1	cis	Heart Left Ventricle	GTEx
rs6823184	NFXL1	cis	Whole Blood	GTEx
rs6823184	CNGA1	cis	Adipose Subcutaneous	GTEx
rs6823184	CORIN	cis	Whole Blood	GTEx
rs6823184	RP11-121C2.2	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:47833200-47840800	Active TSS	Right Atrium	heart
2	chr4:47838000-47840000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr4:47838000-47840200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr4:47838000-47840200	Flanking Active TSS	Duodenum Mucosa	Duodenum
5	chr4:47838000-47840200	Flanking Active TSS	GM12878-XiMat	blood
6	chr4:47838200-47839200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr4:47838200-47839200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr4:47838200-47839200	Flanking Active TSS	Osteobl	bone
9	chr4:47838200-47839400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
10	chr4:47838200-47839400	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 29	rectum
11	chr4:47838200-47839400	Flanking Active TSS	HSMM	muscle
12	chr4:47838200-47839600	Flanking Active TSS	Brain Cingulate Gyrus	brain
13	chr4:47838200-47839800	Active TSS	Breast Myoepithelial Primary Cells	Breast
14	chr4:47838200-47839800	Active TSS	A549	lung
15	chr4:47838200-47839800	Flanking Bivalent TSS/Enh	HUVEC	blood vessel
16	chr4:47838200-47840000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
17	chr4:47838200-47840200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
18	chr4:47838200-47840200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
19	chr4:47838200-47840200	Active TSS	Duodenum Smooth Muscle	Duodenum
20	chr4:47838200-47840200	Active TSS	NHLF	lung
21	chr4:47838200-47840400	Flanking Active TSS	Primary hematopoietic stem cells	blood
22	chr4:47838200-47840400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr4:47838400-47839200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
24	chr4:47838400-47839200	Flanking Bivalent TSS/Enh	Fetal Brain Male	brain
25	chr4:47838400-47839400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr4:47838400-47839400	Active TSS	iPS-15b Cell Line	embryonic stem cell
27	chr4:47838400-47839600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr4:47838400-47839600	Flanking Bivalent TSS/Enh	Primary Natural Killer cells fromperipheralblood	blood
29	chr4:47838400-47839600	Flanking Bivalent TSS/Enh	Primary mononuclear cells fromperipheralblood	Blood
30	chr4:47838400-47839600	Active TSS	Fetal Lung	lung
31	chr4:47838400-47839600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
32	chr4:47838400-47839800	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
33	chr4:47838400-47839800	Active TSS	Colon Smooth Muscle	Colon
34	chr4:47838400-47839800	Active TSS	Pancreatic Islets	Pancreatic Islet
35	chr4:47838400-47839800	Flanking Active TSS	HMEC	breast
36	chr4:47838400-47840000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr4:47838400-47840000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr4:47838400-47840000	Flanking Active TSS	Primary B cells from peripheral blood	blood
39	chr4:47838400-47840000	Active TSS	Primary T helper naive cells from peripheral blood	blood
40	chr4:47838400-47840000	Flanking Active TSS	Adipose Nuclei	Adipose
41	chr4:47838400-47840000	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
42	chr4:47838400-47840000	Active TSS	Ovary	ovary
43	chr4:47838400-47840000	Active TSS	Rectal Smooth Muscle	rectum
44	chr4:47838400-47840200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
45	chr4:47838400-47840200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
46	chr4:47838400-47840200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
47	chr4:47838400-47840200	Active TSS	Muscle Satellite Cultured Cells	--
48	chr4:47838400-47840200	Active TSS	Aorta	Aorta
49	chr4:47838400-47840200	Active TSS	Thymus	Thymus
50	chr4:47838400-47840200	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood

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