Variant report

Variant	rs7606104
Chromosome Location	chr2:48579778-48579779
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:48578562..48582388-chr2:48582784..48586939,6	K562	blood:
2	chr2:48578681..48582388-chr2:48582784..48586647,4	K562	blood:

Extended variants
information (count: 144 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:139)

rs_ID	r²[population]
rs10153773	0.87[JPT][hapmap]
rs10169629	0.91[ASN][1000 genomes]
rs10174717	0.91[AMR][1000 genomes]
rs10186237	0.92[CEU][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes]
rs10199431	0.92[CEU][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10208124	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10208627	0.83[ASN][1000 genomes]
rs10454133	0.89[CEU][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.81[EUR][1000 genomes]
rs10454134	0.83[JPT][hapmap]
rs10495951	0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10495952	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11676036	0.81[ASN][1000 genomes]
rs11676168	0.94[ASW][hapmap];0.92[CEU][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap];0.81[LWK][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];0.85[TSI][hapmap];0.81[YRI][hapmap];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11679523	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs11680719	0.87[JPT][hapmap]
rs11680916	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs11682044	0.88[ASW][hapmap];0.85[CEU][hapmap];0.83[JPT][hapmap];0.95[MEX][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11682633	0.93[ASN][1000 genomes]
rs11682931	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11683099	0.91[ASN][1000 genomes]
rs11683639	0.87[JPT][hapmap]
rs11685861	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11686007	0.87[ASN][1000 genomes]
rs11687708	0.83[ASN][1000 genomes]
rs11688481	0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11689622	0.87[JPT][hapmap]
rs11689645	0.90[ASN][1000 genomes]
rs11690690	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11690748	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11690845	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12052754	0.92[ASN][1000 genomes]
rs12105983	0.83[ASN][1000 genomes]
rs12328506	0.92[ASN][1000 genomes]
rs13383364	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13385535	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13386751	0.81[EUR][1000 genomes]
rs13387171	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13388291	0.92[CEU][hapmap];0.86[JPT][hapmap];0.86[TSI][hapmap];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs13392004	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13398791	0.92[ASN][1000 genomes]
rs13401749	0.87[JPT][hapmap]
rs13432998	0.81[CEU][hapmap];0.85[GIH][hapmap];0.87[JPT][hapmap];0.85[MEX][hapmap];0.83[TSI][hapmap];0.82[YRI][hapmap];0.88[AMR][1000 genomes]
rs17037289	0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs17037298	0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs17855177	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs28841370	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4290706	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4316980	0.87[JPT][hapmap]
rs4344965	0.92[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4411759	0.92[CEU][hapmap];0.87[JPT][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap];0.82[YRI][hapmap];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4438532	0.83[JPT][hapmap]
rs4497915	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs4547570	0.92[ASN][1000 genomes]
rs4547573	0.89[CEU][hapmap];0.96[YRI][hapmap]
rs4606978	0.83[JPT][hapmap]
rs4641990	0.91[JPT][hapmap];0.88[YRI][hapmap]
rs55660911	0.97[ASN][1000 genomes]
rs55744465	0.89[ASN][1000 genomes]
rs55761545	0.92[ASN][1000 genomes]
rs55788229	0.82[ASN][1000 genomes]
rs56156294	0.89[ASN][1000 genomes]
rs56163539	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56365822	0.81[ASN][1000 genomes]
rs56391806	0.89[ASN][1000 genomes]
rs57131168	0.86[ASN][1000 genomes]
rs57537506	0.97[ASN][1000 genomes]
rs57668696	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs57893565	0.96[ASN][1000 genomes]
rs58012056	0.98[ASN][1000 genomes]
rs59045263	0.83[ASN][1000 genomes]
rs59697023	0.85[ASN][1000 genomes]
rs59761994	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs60042255	0.81[ASN][1000 genomes]
rs60815228	0.84[ASN][1000 genomes]
rs60825643	0.91[ASN][1000 genomes]
rs61303367	0.81[ASN][1000 genomes]
rs62136987	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62137002	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62137003	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62137015	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62137019	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62137041	0.81[AMR][1000 genomes]
rs62138801	0.81[EUR][1000 genomes]
rs6545026	0.92[YRI][hapmap]
rs6545027	0.88[CEU][hapmap];0.82[JPT][hapmap];0.92[YRI][hapmap]
rs6545030	0.96[CEU][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6545034	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6545035	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6545036	0.83[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.96[YRI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6545039	0.88[EUR][1000 genomes]
rs66705539	0.83[ASN][1000 genomes]
rs6705802	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.96[ASN][1000 genomes]
rs6712029	0.96[CEU][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.82[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6718068	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6722246	0.96[ASN][1000 genomes]
rs6735288	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6743757	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6745580	0.94[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs6749773	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6756596	0.93[ASN][1000 genomes]
rs6757206	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs72818488	0.86[ASN][1000 genomes]
rs72818491	0.84[ASN][1000 genomes]
rs72818493	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs72818494	0.84[ASN][1000 genomes]
rs72818502	0.90[ASN][1000 genomes]
rs72820403	0.94[ASN][1000 genomes]
rs72820404	0.96[ASN][1000 genomes]
rs72820405	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72820409	0.97[ASN][1000 genomes]
rs72820411	0.96[ASN][1000 genomes]
rs72820415	0.96[ASN][1000 genomes]
rs72820416	0.96[ASN][1000 genomes]
rs72820418	0.96[ASN][1000 genomes]
rs72820420	0.97[ASN][1000 genomes]
rs72820422	0.99[ASN][1000 genomes]
rs72820423	0.98[ASN][1000 genomes]
rs72820424	0.95[ASN][1000 genomes]
rs72820427	0.95[ASN][1000 genomes]
rs72820433	0.93[ASN][1000 genomes]
rs72820436	0.94[ASN][1000 genomes]
rs72820437	0.96[ASN][1000 genomes]
rs72820439	0.96[ASN][1000 genomes]
rs72820441	0.92[ASN][1000 genomes]
rs72820445	0.96[ASN][1000 genomes]
rs72820454	0.81[ASN][1000 genomes]
rs72887649	0.82[AMR][1000 genomes]
rs7559431	0.91[ASN][1000 genomes]
rs7562069	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7562816	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7566239	0.91[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.80[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs7568574	0.82[ASN][1000 genomes]
rs7568960	0.80[EUR][1000 genomes]
rs7573316	0.88[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs7576964	0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.90[LWK][hapmap];0.82[MEX][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs7577237	0.82[ASW][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs7579932	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7600794	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9309152	0.83[AMR][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7606104	PPP1R21	cis	Thyroid	GTEx

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48569000-48580000	Weak transcription	Rectal Smooth Muscle	rectum
2	chr2:48571200-48605200	Weak transcription	Colonic Mucosa	Colon
3	chr2:48571600-48580000	Weak transcription	Stomach Smooth Muscle	stomach
4	chr2:48572200-48597000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr2:48572400-48580000	Weak transcription	Stomach Mucosa	stomach
6	chr2:48573400-48583200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr2:48573600-48604000	Weak transcription	Ovary	ovary
8	chr2:48574200-48581000	Genic enhancers	HepG2	liver
9	chr2:48574200-48602000	Weak transcription	Gastric	stomach
10	chr2:48574600-48602000	Weak transcription	Small Intestine	intestine
11	chr2:48574800-48589600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr2:48574800-48589600	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr2:48576200-48579800	Weak transcription	NH-A	brain
14	chr2:48576200-48580000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr2:48576200-48580400	Weak transcription	Left Ventricle	heart
16	chr2:48576200-48583800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr2:48576200-48597000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr2:48576200-48602000	Weak transcription	Lung	lung
19	chr2:48576400-48579800	Enhancers	Primary T helper cells PMA-I stimulated	--
20	chr2:48576400-48579800	Weak transcription	Hela-S3	cervix
21	chr2:48576400-48580200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
22	chr2:48576400-48583800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
23	chr2:48576400-48590000	Weak transcription	Placenta	Placenta
24	chr2:48576600-48581400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
25	chr2:48576600-48595600	Weak transcription	Fetal Brain Female	brain
26	chr2:48576600-48602000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr2:48577000-48579800	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr2:48577000-48580200	Weak transcription	Fetal Lung	lung
29	chr2:48577000-48580400	Enhancers	Primary T helper naive cells from peripheral blood	blood
30	chr2:48577000-48580800	Enhancers	Brain Anterior Caudate	brain
31	chr2:48577000-48581400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
32	chr2:48577000-48583800	Enhancers	Primary T helper cells fromperipheralblood	blood
33	chr2:48577200-48580200	Enhancers	Brain Substantia Nigra	brain
34	chr2:48577200-48581600	Enhancers	Brain Hippocampus Middle	brain
35	chr2:48577600-48579800	Strong transcription	K562	blood
36	chr2:48577600-48580000	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr2:48577600-48581600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
38	chr2:48577600-48584200	Weak transcription	Thymus	Thymus
39	chr2:48577600-48589600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr2:48577600-48589600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr2:48577800-48579800	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr2:48577800-48592400	Weak transcription	Right Atrium	heart
43	chr2:48577800-48602000	Weak transcription	Fetal Kidney	kidney
44	chr2:48577800-48603800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr2:48578000-48579800	Enhancers	Monocytes-CD14+_RO01746	blood
46	chr2:48578000-48580000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr2:48578000-48580000	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr2:48578000-48580400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr2:48578200-48579800	Weak transcription	HSMM	muscle
50	chr2:48578200-48584400	Weak transcription	Fetal Thymus	thymus

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