Variant report

Variant	rs35199727
Chromosome Location	chr3:47946708-47946709
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	chr3:47940250..47943002-chr3:47945060..47946714,2	K562	blood:

Extended variants
information (count: 117 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs1013431	0.88[EUR][1000 genomes]
rs1060407	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1061003	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11130150	0.81[ASN][1000 genomes]
rs11130152	0.86[EUR][1000 genomes]
rs11130154	0.89[EUR][1000 genomes]
rs1137524	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11707679	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13074973	0.89[EUR][1000 genomes]
rs13075457	0.86[EUR][1000 genomes]
rs13075795	0.87[EUR][1000 genomes]
rs13077230	0.81[ASN][1000 genomes]
rs13081701	0.86[EUR][1000 genomes]
rs13093830	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1530646	0.89[EUR][1000 genomes]
rs1550914	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1665982	0.91[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs1684942	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17290490	0.81[ASN][1000 genomes]
rs184388	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2053767	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2121754	0.89[EUR][1000 genomes]
rs2166770	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2166772	0.89[EUR][1000 genomes]
rs2631721	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28637561	0.89[EUR][1000 genomes]
rs2882668	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs319680	0.82[EUR][1000 genomes]
rs319681	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs319682	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs319684	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs319685	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs319686	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs319687	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs319688	0.94[EUR][1000 genomes]
rs319689	0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs319690	0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs319691	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs319692	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs319693	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs319694	0.81[ASN][1000 genomes]
rs319695	0.91[ASN][1000 genomes]
rs319696	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34025851	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34750113	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35314534	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35582375	0.81[ASN][1000 genomes]
rs35689209	0.84[EUR][1000 genomes]
rs35943823	0.86[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs3732529	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4293721	0.89[EUR][1000 genomes]
rs4296617	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4392441	0.87[EUR][1000 genomes]
rs4599334	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4858863	0.84[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs4858871	0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4858876	0.84[EUR][1000 genomes]
rs4858880	0.83[EUR][1000 genomes]
rs4858881	0.82[EUR][1000 genomes]
rs4858887	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs5012971	0.87[EUR][1000 genomes]
rs60446735	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62260764	0.82[EUR][1000 genomes]
rs6442090	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6442091	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6442094	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6442096	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6442101	0.83[EUR][1000 genomes]
rs6770467	0.89[EUR][1000 genomes]
rs6770477	0.89[EUR][1000 genomes]
rs6772396	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6773208	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6783629	0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6791834	0.85[EUR][1000 genomes]
rs6803741	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6806820	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7374516	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7426976	0.89[EUR][1000 genomes]
rs7427418	0.89[EUR][1000 genomes]
rs7429990	0.82[EUR][1000 genomes]
rs7430879	0.89[EUR][1000 genomes]
rs7430913	0.89[EUR][1000 genomes]
rs7431567	0.81[AMR][1000 genomes]
rs7619882	0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7620736	0.85[EUR][1000 genomes]
rs7627645	0.87[EUR][1000 genomes]
rs7629850	0.84[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs7642590	0.86[EUR][1000 genomes]
rs7649981	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7653368	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs777014	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs777015	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs777017	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs796566	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs800762	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs810334	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9811277	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9812875	0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9814961	0.89[EUR][1000 genomes]
rs9842649	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9846062	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9850154	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs9854454	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9860485	0.86[EUR][1000 genomes]
rs9862913	0.89[EUR][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	nsv1006560	chr3:47867461-48037031	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	141 gene(s)	inside rSNPs	diseases
2	nsv1011662	chr3:47891634-48019462	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv536561	chr3:47891634-48019462	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
4	nsv529989	chr3:47909480-48301481	Genic enhancers Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats 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 miRNA target site	42 gene(s)	inside rSNPs	diseases
5	nsv1001056	chr3:47912342-48223849	Genic enhancers Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
6	esv1796001	chr3:47912703-48012797	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	esv1826403	chr3:47912703-48012797	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	esv1835684	chr3:47912703-48123540	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
9	esv1827272	chr3:47912703-48260968	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
10	nsv1000817	chr3:47927730-48032401	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
11	nsv1009243	chr3:47935331-48340448	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
12	nsv536562	chr3:47935331-48340448	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs35199727	NME6	cis	Esophagus Muscularis	GTEx
rs35199727	ZNF589	cis	Nerve Tibial	GTEx
rs35199727	MRPS18AP1	cis	Artery Tibial	GTEx
rs35199727	ZNF589	cis	Whole Blood	GTEx
rs35199727	MRPS18AP1	cis	Thyroid	GTEx
rs35199727	MRPS18AP1	cis	Nerve Tibial	GTEx
rs35199727	MAP4	Cis_1M	lymphoblastoid	RTeQTL
rs35199727	DHX30	Cis_1M	lymphoblastoid	RTeQTL
rs35199727	MRPS18AP1	cis	Muscle Skeletal	GTEx

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47910200-47957000	Weak transcription	Small Intestine	intestine
2	chr3:47910200-47978000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr3:47917600-47957400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr3:47922000-47951400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr3:47926800-47953400	Weak transcription	Primary hematopoietic stem cells	blood
6	chr3:47926800-47957400	Weak transcription	Colonic Mucosa	Colon
7	chr3:47932000-47969200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr3:47933200-47953200	Weak transcription	Fetal Kidney	kidney
9	chr3:47933800-47948400	Weak transcription	Primary B cells from peripheral blood	blood
10	chr3:47933800-47952200	Weak transcription	Psoas Muscle	Psoas
11	chr3:47933800-47953000	Weak transcription	Primary neutrophils fromperipheralblood	blood
12	chr3:47934000-47952400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr3:47934000-47952400	Weak transcription	Spleen	Spleen
14	chr3:47934000-47952800	Weak transcription	Primary monocytes fromperipheralblood	blood
15	chr3:47934200-47950400	Weak transcription	HUVEC	blood vessel
16	chr3:47934200-47951000	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr3:47934200-47952000	Weak transcription	Ovary	ovary
18	chr3:47934200-47952400	Weak transcription	Esophagus	oesophagus
19	chr3:47934200-47952600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr3:47934200-47953400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr3:47934200-47957200	Weak transcription	Gastric	stomach
22	chr3:47934400-47950600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr3:47934400-47952200	Weak transcription	A549	lung
24	chr3:47934600-47951200	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr3:47934800-47956800	Weak transcription	Fetal Brain Female	brain
26	chr3:47935000-47949000	Weak transcription	Primary B cells from cord blood	blood
27	chr3:47935200-47951000	Weak transcription	Brain Anterior Caudate	brain
28	chr3:47935200-47953200	Weak transcription	Brain Germinal Matrix	brain
29	chr3:47935200-47957200	Weak transcription	Brain Cingulate Gyrus	brain
30	chr3:47935400-47949000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr3:47935600-47949200	Weak transcription	K562	blood
32	chr3:47935600-47952200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr3:47935800-47952600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr3:47935800-47956200	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr3:47935800-47956800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr3:47936800-47951200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr3:47937000-47949200	Weak transcription	Hela-S3	cervix
38	chr3:47937200-47951000	Weak transcription	Rectal Smooth Muscle	rectum
39	chr3:47937400-47950400	Weak transcription	Fetal Lung	lung
40	chr3:47937400-47953400	Weak transcription	Thymus	Thymus
41	chr3:47937600-47950400	Weak transcription	NHLF	lung
42	chr3:47937600-47952400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr3:47938600-47953200	Weak transcription	Brain Substantia Nigra	brain
44	chr3:47939200-47951800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr3:47939800-47952000	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr3:47940000-47947400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr3:47940200-47949000	Weak transcription	Primary T cells from cord blood	blood
48	chr3:47940200-47950600	Weak transcription	Fetal Thymus	thymus
49	chr3:47940200-47952000	Weak transcription	Dnd41	blood
50	chr3:47940200-47952400	Weak transcription	Primary T helper cells PMA-I stimulated	--

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