Variant report

Variant	rs9860485
Chromosome Location	chr3:48014205-48014206
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	chr3:48013205..48014837-chr3:48015200..48018193,2	MCF-7	breast:
2	chr12:94728960..94729681-chr3:48014076..48014912,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000173588	Chromatin interaction

Extended variants
information (count: 128 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:115)

rs_ID	r²[population]
rs1013431	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1060407	0.86[EUR][1000 genomes]
rs1061003	0.80[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs11130152	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11130154	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11130155	0.84[EUR][1000 genomes]
rs1137524	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11707679	0.86[EUR][1000 genomes]
rs11710866	0.84[EUR][1000 genomes]
rs11711129	0.84[EUR][1000 genomes]
rs11714518	0.81[EUR][1000 genomes]
rs11720151	0.84[EUR][1000 genomes]
rs11924107	0.82[EUR][1000 genomes]
rs12486714	0.82[EUR][1000 genomes]
rs12493348	0.84[EUR][1000 genomes]
rs13074973	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13075457	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13075795	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13080997	0.82[EUR][1000 genomes]
rs13081463	0.84[EUR][1000 genomes]
rs13093830	0.86[EUR][1000 genomes]
rs1530646	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1550914	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1684942	0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs17290490	0.81[AFR][1000 genomes]
rs184388	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2053767	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2121754	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2166770	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2166772	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2361683	0.82[EUR][1000 genomes]
rs2361684	0.82[EUR][1000 genomes]
rs2631721	0.82[AFR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28637561	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2882668	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs319681	0.82[EUR][1000 genomes]
rs319682	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs319684	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs319685	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs319686	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs319687	0.83[AFR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs319688	0.81[EUR][1000 genomes]
rs319689	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs319690	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs319691	0.81[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs319692	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs319694	0.81[AFR][1000 genomes]
rs319696	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34025851	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34597784	0.82[EUR][1000 genomes]
rs34750113	0.87[EUR][1000 genomes]
rs35199727	0.86[EUR][1000 genomes]
rs35314534	0.98[EUR][1000 genomes]
rs35689209	0.93[EUR][1000 genomes]
rs3732529	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4293721	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4296617	0.98[EUR][1000 genomes]
rs4392441	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4599334	0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4858871	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4858876	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4858880	0.92[EUR][1000 genomes]
rs4858881	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4858882	0.85[EUR][1000 genomes]
rs4858887	0.96[EUR][1000 genomes]
rs5012971	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56067795	0.82[EUR][1000 genomes]
rs60446735	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6442090	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6442091	0.98[EUR][1000 genomes]
rs6442094	0.91[EUR][1000 genomes]
rs6442096	0.92[EUR][1000 genomes]
rs6442101	0.92[EUR][1000 genomes]
rs6442102	0.82[EUR][1000 genomes]
rs6766641	0.84[EUR][1000 genomes]
rs6768318	0.85[EUR][1000 genomes]
rs6770467	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6770477	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6772396	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6773208	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6777081	0.81[EUR][1000 genomes]
rs6783629	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6791834	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6803741	0.93[EUR][1000 genomes]
rs6806820	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7374482	0.81[EUR][1000 genomes]
rs7374516	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7426976	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7427418	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7427648	0.81[EUR][1000 genomes]
rs7430879	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7430913	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7618163	0.81[EUR][1000 genomes]
rs7619882	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7620736	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7627645	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7642590	0.93[EUR][1000 genomes]
rs7649981	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7651237	0.81[EUR][1000 genomes]
rs7653368	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs777015	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs777017	0.86[EUR][1000 genomes]
rs796566	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs800762	0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs810334	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs936428	0.81[EUR][1000 genomes]
rs9811277	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9812875	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9814961	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9825114	0.85[EUR][1000 genomes]
rs9828959	0.86[EUR][1000 genomes]
rs9842649	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9846062	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9854454	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9862913	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[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	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	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
7	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
8	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
9	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
10	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
11	nsv1012828	chr3:47996472-48192862	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
12	nsv1002067	chr3:47996472-48326518	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
13	esv3335628	chr3:48010796-48074001	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs9860485	NME6	cis	Esophagus Muscularis	GTEx
rs9860485	DHX30	Cis_1M	lymphoblastoid	RTeQTL
rs9860485	MRPS18AP1	cis	lung	GTEx
rs9860485	ZNF589	cis	Nerve Tibial	GTEx
rs9860485	MRPS18AP1	cis	Nerve Tibial	GTEx
rs9860485	ZNF589	cis	Artery Tibial	GTEx
rs9860485	MRPS18AP1	cis	Thyroid	GTEx
rs9860485	MAP4	Cis_1M	lymphoblastoid	RTeQTL
rs9860485	MRPS18AP1	cis	Artery Tibial	GTEx
rs9860485	MRPS18AP1	cis	Muscle Skeletal	GTEx

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47970200-48016600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr3:47991600-48016800	Weak transcription	Fetal Intestine Large	intestine
3	chr3:47996400-48018400	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr3:47996600-48014600	Weak transcription	NH-A	brain
5	chr3:47996800-48016000	Weak transcription	HUVEC	blood vessel
6	chr3:47998200-48031400	Weak transcription	Brain Germinal Matrix	brain
7	chr3:48003400-48015000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr3:48003400-48017800	Weak transcription	Stomach Smooth Muscle	stomach
9	chr3:48003400-48029000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr3:48003800-48014400	Weak transcription	HSMM	muscle
11	chr3:48003800-48014800	Weak transcription	Aorta	Aorta
12	chr3:48003800-48017800	Weak transcription	Dnd41	blood
13	chr3:48003800-48018200	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr3:48003800-48025600	Weak transcription	Adipose Nuclei	Adipose
15	chr3:48003800-48028400	Weak transcription	Fetal Kidney	kidney
16	chr3:48003800-48032800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr3:48003800-48034400	Weak transcription	Fetal Lung	lung
18	chr3:48003800-48034600	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr3:48003800-48037200	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr3:48003800-48039800	Weak transcription	Brain Angular Gyrus	brain
21	chr3:48003800-48047200	Weak transcription	Lung	lung
22	chr3:48003800-48060600	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr3:48004000-48016600	Weak transcription	Fetal Muscle Leg	muscle
24	chr3:48004000-48016800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr3:48004000-48016800	Weak transcription	Thymus	Thymus
26	chr3:48004000-48017400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr3:48004000-48017600	Weak transcription	Fetal Thymus	thymus
28	chr3:48004000-48021000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr3:48004000-48022400	Weak transcription	Fetal Heart	heart
30	chr3:48004000-48024600	Weak transcription	Right Atrium	heart
31	chr3:48004000-48031400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr3:48004000-48031400	Weak transcription	Fetal Intestine Small	intestine
33	chr3:48004000-48037200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr3:48004000-48037200	Weak transcription	Primary T cells fromperipheralblood	blood
35	chr3:48004000-48037400	Weak transcription	Right Ventricle	heart
36	chr3:48004000-48043600	Weak transcription	Small Intestine	intestine
37	chr3:48004000-48045400	Weak transcription	Placenta	Placenta
38	chr3:48004000-48046200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr3:48004000-48050600	Weak transcription	Pancreas	Pancrea
40	chr3:48004200-48018800	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr3:48004200-48025200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr3:48004200-48028400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr3:48004400-48025400	Weak transcription	NHLF	lung
44	chr3:48004600-48016400	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr3:48004600-48018200	Weak transcription	Brain Hippocampus Middle	brain
46	chr3:48004600-48025200	Weak transcription	Hela-S3	cervix
47	chr3:48004600-48031000	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr3:48004600-48035400	Weak transcription	Primary T helper cells fromperipheralblood	blood
49	chr3:48004800-48025600	Weak transcription	HMEC	breast
50	chr3:48004800-48031200	Weak transcription	Rectal Smooth Muscle	rectum

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