Variant report

Variant	rs6756596
Chromosome Location	chr2:48610367-48610368
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:48601929..48604341-chr2:48608996..48611918,2	MCF-7	breast:

Extended variants
information (count: 113 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:108)

rs_ID	r²[population]
rs10153773	0.87[JPT][hapmap]
rs10169629	0.97[ASN][1000 genomes]
rs10199431	0.87[JPT][hapmap]
rs10208627	0.89[ASN][1000 genomes]
rs10454133	0.83[CHD][hapmap];0.83[JPT][hapmap]
rs10454134	0.83[JPT][hapmap]
rs10495951	1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10495952	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11676168	0.91[JPT][hapmap]
rs11679523	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.96[ASN][1000 genomes]
rs11680719	0.87[JPT][hapmap]
rs11680916	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11682044	0.83[JPT][hapmap]
rs11682633	0.89[ASN][1000 genomes]
rs11683099	0.80[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs11683639	0.83[CEU][hapmap];0.87[JPT][hapmap];0.81[MEX][hapmap]
rs11685861	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11686007	0.83[ASN][1000 genomes]
rs11688481	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11689622	0.83[CEU][hapmap];0.87[JPT][hapmap]
rs11689645	0.94[ASN][1000 genomes]
rs11690690	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11690748	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11690845	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs12052754	0.94[ASN][1000 genomes]
rs12105983	0.89[ASN][1000 genomes]
rs12328506	0.97[ASN][1000 genomes]
rs13388291	0.86[JPT][hapmap]
rs13398791	0.97[ASN][1000 genomes]
rs13401749	0.83[CEU][hapmap];0.87[JPT][hapmap];0.81[MEX][hapmap]
rs13432998	0.87[JPT][hapmap]
rs17037289	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs17037298	0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.94[ASN][1000 genomes]
rs17855177	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4316980	0.87[JPT][hapmap]
rs4344965	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.96[ASN][1000 genomes]
rs4411759	0.87[JPT][hapmap]
rs4438532	0.83[JPT][hapmap]
rs4547570	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4606978	0.84[CHD][hapmap];0.83[JPT][hapmap]
rs4641990	0.91[JPT][hapmap]
rs55660911	0.96[ASN][1000 genomes]
rs55744465	0.94[ASN][1000 genomes]
rs55761545	0.88[ASN][1000 genomes]
rs56156294	0.94[ASN][1000 genomes]
rs56163539	0.85[ASN][1000 genomes]
rs56365822	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56391806	0.94[ASN][1000 genomes]
rs57131168	0.82[ASN][1000 genomes]
rs57537506	0.93[ASN][1000 genomes]
rs57893565	0.97[ASN][1000 genomes]
rs58012056	0.95[ASN][1000 genomes]
rs58978223	0.84[ASN][1000 genomes]
rs59045263	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59697023	0.81[ASN][1000 genomes]
rs60042255	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60825643	0.97[ASN][1000 genomes]
rs61303367	0.86[ASN][1000 genomes]
rs62137015	0.96[ASN][1000 genomes]
rs62137018	0.84[ASN][1000 genomes]
rs62137019	0.86[ASN][1000 genomes]
rs62137021	0.86[ASN][1000 genomes]
rs6545027	0.82[JPT][hapmap]
rs6545030	0.91[JPT][hapmap]
rs6545036	0.91[CHB][hapmap];0.95[CHD][hapmap];0.83[JPT][hapmap];0.88[ASN][1000 genomes]
rs66705539	0.88[ASN][1000 genomes]
rs6705802	1.00[CHB][hapmap];0.98[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6712029	0.91[JPT][hapmap]
rs6718068	1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6722246	0.97[ASN][1000 genomes]
rs6735288	0.88[ASN][1000 genomes]
rs6743757	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.96[ASN][1000 genomes]
rs6745580	0.93[ASN][1000 genomes]
rs6747441	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6749773	0.86[ASN][1000 genomes]
rs72818488	0.82[ASN][1000 genomes]
rs72818494	0.81[ASN][1000 genomes]
rs72818502	0.86[ASN][1000 genomes]
rs72820403	0.90[ASN][1000 genomes]
rs72820404	0.92[ASN][1000 genomes]
rs72820409	0.92[ASN][1000 genomes]
rs72820411	0.92[ASN][1000 genomes]
rs72820415	0.92[ASN][1000 genomes]
rs72820416	0.92[ASN][1000 genomes]
rs72820418	0.92[ASN][1000 genomes]
rs72820420	0.93[ASN][1000 genomes]
rs72820422	0.94[ASN][1000 genomes]
rs72820423	0.95[ASN][1000 genomes]
rs72820424	0.92[ASN][1000 genomes]
rs72820427	0.96[ASN][1000 genomes]
rs72820433	0.96[ASN][1000 genomes]
rs72820436	0.96[ASN][1000 genomes]
rs72820437	0.97[ASN][1000 genomes]
rs72820439	0.97[ASN][1000 genomes]
rs72820441	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72820445	0.97[ASN][1000 genomes]
rs72820454	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7559431	0.92[ASN][1000 genomes]
rs7562069	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7562816	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.96[ASN][1000 genomes]
rs7566239	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7568574	0.87[ASN][1000 genomes]
rs7573316	0.97[ASN][1000 genomes]
rs7576964	1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs7577237	1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7579932	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7600794	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7606104	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530831	chr2:48059709-48632317	Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv874001	chr2:48534363-48624007	Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv874002	chr2:48547751-48610367	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases
4	esv2762252	chr2:48554150-48741093	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	nsv874003	chr2:48570509-48619869	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6756596	PPP1R21	cis	Thyroid	GTEx
rs6756596	CCDC128	Cis_1M	lymphoblastoid	RTeQTL
rs6756596	FOXN2	cis	parietal	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48598600-48612800	Weak transcription	Fetal Stomach	stomach
2	chr2:48602600-48612000	Weak transcription	Lung	lung
3	chr2:48602600-48612800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr2:48602600-48613400	Weak transcription	Left Ventricle	heart
5	chr2:48602800-48612800	Weak transcription	Fetal Muscle Trunk	muscle
6	chr2:48603800-48614800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr2:48605200-48615000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr2:48605800-48615800	Weak transcription	Dnd41	blood
9	chr2:48607200-48611800	Weak transcription	Adipose Nuclei	Adipose
10	chr2:48607400-48611600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr2:48607800-48612800	Weak transcription	HUVEC	blood vessel
12	chr2:48608400-48610400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr2:48608400-48613200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr2:48608400-48618000	Weak transcription	Brain Cingulate Gyrus	brain
15	chr2:48609600-48611000	Enhancers	Primary monocytes fromperipheralblood	blood
16	chr2:48610000-48610600	Enhancers	Primary hematopoietic stem cells short term culture	blood
17	chr2:48610200-48610400	Enhancers	Primary B cells from cord blood	blood
18	chr2:48610200-48610400	Enhancers	Monocytes-CD14+_RO01746	blood
19	chr2:48610200-48610600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
20	chr2:48610200-48610600	Enhancers	Primary B cells from peripheral blood	blood
21	chr2:48610200-48610600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr2:48610200-48610600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr2:48610200-48610800	Enhancers	Primary hematopoietic stem cells	blood

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