Variant report

Variant	rs311584
Chromosome Location	chr2:86285146-86285147
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	chr2:86283452..86286024-chr2:86293941..86297049,3	MCF-7	breast:

Extended variants
information (count: 60 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10187875	1.00[ASN][1000 genomes]
rs10779967	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11127015	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11885520	0.91[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs11886175	1.00[ASN][1000 genomes]
rs11890563	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11891096	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11895453	0.92[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12473739	1.00[ASN][1000 genomes]
rs13353	0.91[ASN][1000 genomes]
rs13390107	1.00[ASN][1000 genomes]
rs13420958	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13431245	0.92[ASN][1000 genomes]
rs1424516	1.00[ASN][1000 genomes]
rs1469982	0.92[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2059353	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2288117	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs311561	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs311570	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs311580	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs311581	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs311582	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs311583	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs311586	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs34892520	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3770073	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3810828	1.00[ASN][1000 genomes]
rs4832027	1.00[ASN][1000 genomes]
rs4832028	0.91[ASN][1000 genomes]
rs4832239	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4832254	1.00[ASN][1000 genomes]
rs57339071	1.00[ASN][1000 genomes]
rs58077381	0.92[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6707736	0.92[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs6715623	1.00[ASN][1000 genomes]
rs6720431	1.00[ASN][1000 genomes]
rs6723248	1.00[ASN][1000 genomes]
rs6749218	1.00[ASN][1000 genomes]
rs6752561	1.00[ASN][1000 genomes]
rs72847843	0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72847853	1.00[ASN][1000 genomes]
rs7340327	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7419344	0.91[ASN][1000 genomes]
rs7558040	1.00[ASN][1000 genomes]
rs7583021	0.91[ASN][1000 genomes]
rs7592211	0.91[ASN][1000 genomes]
rs7597608	0.82[ASN][1000 genomes]
rs7599498	0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs889911	0.91[ASN][1000 genomes]
rs918856	1.00[ASN][1000 genomes]
rs929916	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9677675	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9679308	0.80[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs979940	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2751903	chr2:86253542-86505453	Active TSS Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv531380	chr2:86253552-86469217	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats 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	47 gene(s)	inside rSNPs	diseases
3	nsv870120	chr2:86265437-86343058	Strong transcription Genic enhancers Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases
4	nsv1007474	chr2:86281967-86505453	Enhancers Flanking Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
5	nsv997563	chr2:86281967-86506132	Genic enhancers Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
6	nsv1008924	chr2:86282722-86499402	Genic enhancers Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking 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	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs311584	MRPL35	cis	Artery Aorta	GTEx
rs311584	MRPL35	cis	Esophagus Muscularis	GTEx
rs311584	POLR1A	cis	Nerve Tibial	GTEx
rs311584	MRPL35	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86251200-86285200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
2	chr2:86252000-86331200	Strong transcription	HUES64 Cell Line	embryonic stem cell
3	chr2:86252200-86285200	Strong transcription	HUES48 Cell Line	embryonic stem cell
4	chr2:86264000-86332000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr2:86264400-86285400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr2:86264400-86285400	Strong transcription	A549	lung
7	chr2:86265200-86330000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr2:86265400-86285200	Strong transcription	Fetal Intestine Large	intestine
9	chr2:86265400-86289800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr2:86265400-86289800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr2:86265600-86289800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr2:86265800-86305400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr2:86266000-86287800	Weak transcription	Right Atrium	heart
14	chr2:86266400-86288800	Strong transcription	Duodenum Mucosa	Duodenum
15	chr2:86266400-86295800	Weak transcription	Primary neutrophils fromperipheralblood	blood
16	chr2:86266800-86289800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr2:86267200-86290800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr2:86268800-86291000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr2:86268800-86295000	Strong transcription	Dnd41	blood
20	chr2:86269800-86289800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr2:86275200-86289000	Weak transcription	Stomach Mucosa	stomach
22	chr2:86275800-86290000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
23	chr2:86276400-86290000	Weak transcription	Fetal Heart	heart
24	chr2:86276400-86291000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr2:86276800-86291200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr2:86277000-86286200	Weak transcription	Fetal Brain Male	brain
27	chr2:86279600-86285200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr2:86280200-86293000	Weak transcription	Psoas Muscle	Psoas
29	chr2:86280800-86291200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr2:86281200-86288800	Weak transcription	Aorta	Aorta
31	chr2:86281200-86289400	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr2:86281200-86290800	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr2:86281400-86285800	Weak transcription	HUVEC	blood vessel
34	chr2:86281400-86286200	Weak transcription	NHLF	lung
35	chr2:86281400-86287000	Weak transcription	Primary monocytes fromperipheralblood	blood
36	chr2:86281400-86287200	Weak transcription	Liver	Liver
37	chr2:86281400-86287600	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr2:86281400-86288400	Weak transcription	Ovary	ovary
39	chr2:86281400-86290800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr2:86281400-86290800	Weak transcription	Colonic Mucosa	Colon
41	chr2:86281400-86291400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr2:86281400-86292400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr2:86281600-86286200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr2:86281600-86286200	Weak transcription	Brain Anterior Caudate	brain
45	chr2:86281600-86286200	Weak transcription	Hela-S3	cervix
46	chr2:86281600-86286600	Weak transcription	Osteobl	bone
47	chr2:86281600-86287200	Weak transcription	Adipose Nuclei	Adipose
48	chr2:86281600-86287200	Weak transcription	HMEC	breast
49	chr2:86281600-86287200	Weak transcription	NH-A	brain
50	chr2:86281600-86287600	Weak transcription	Fetal Kidney	kidney

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