Variant report

Variant	rs9677675
Chromosome Location	chr2:86268494-86268495
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:86268493-86269034	K562	blood:	n/a	n/a
2	POLR2A	chr2:86268141-86268845	GM12892	blood:	n/a	n/a
3	POLR2A	chr2:86268225-86268599	GM12878	blood:	n/a	n/a
4	POLR2A	chr2:86268176-86268859	K562	blood:	n/a	n/a
5	GATA3	chr2:86268129-86268583	MCF-7	breast:	n/a	n/a
6	GABPA	chr2:86268033-86268595	MCF-7	breast:	n/a	chr2:86268487-86268501 chr2:86268484-86268498
7	POLR2A	chr2:86268152-86268546	H1-hESC	embryonic stem cell:	n/a	n/a
8	GABPA	chr2:86268191-86268568	HepG2	liver:	n/a	chr2:86268487-86268501 chr2:86268484-86268498
9	GABPA	chr2:86268196-86268586	K562	blood:	n/a	chr2:86268487-86268501 chr2:86268484-86268498
10	CTCF	chr2:86268214-86268533	GM12891	blood:	n/a	n/a
11	CTCF	chr2:86268025-86268515	MCF-7	breast:	n/a	n/a
12	POLR2A	chr2:86267736-86268834	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:86263075..86266284-chr2:86266783..86270779,4	MCF-7	breast:

Variant related genes	Relation type
POLR1A	TF binding region
ENSG00000068654	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10187875	1.00[ASN][1000 genomes]
rs10779967	1.00[ASN][1000 genomes]
rs11127015	1.00[ASN][1000 genomes]
rs11885520	0.81[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs11886175	1.00[ASN][1000 genomes]
rs11890563	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11891096	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11895453	0.82[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	0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2059353	1.00[ASN][1000 genomes]
rs2288117	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs311561	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs311570	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs311580	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs311581	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs311582	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs311583	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs311584	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34892520	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3770073	0.84[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	1.00[ASN][1000 genomes]
rs4832254	1.00[ASN][1000 genomes]
rs57339071	1.00[ASN][1000 genomes]
rs58077381	0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6707736	0.82[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	1.00[ASN][1000 genomes]
rs72847853	1.00[ASN][1000 genomes]
rs7340327	0.87[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	1.00[ASN][1000 genomes]
rs889911	0.91[ASN][1000 genomes]
rs918856	1.00[ASN][1000 genomes]
rs929916	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9679308	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	nsv1001104	chr2:86182021-86271923	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv535807	chr2:86182021-86271923	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	esv3525773	chr2:86268386-86268627	Strong transcription Genic enhancers Weak transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9677675	MRPL35	cis	Esophagus Muscularis	GTEx
rs9677675	MRPL35	Cis_1M	lymphoblastoid	RTeQTL
rs9677675	MRPL35	cis	Artery Aorta	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86251200-86273200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
2	chr2:86251200-86281400	Strong transcription	H9 Cell Line	embryonic stem cell
3	chr2:86251200-86283000	Strong transcription	HepG2	liver
4	chr2:86251200-86283200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr2:86251200-86285000	Strong transcription	HUES6 Cell Line	embryonic stem cell
6	chr2:86251200-86285200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
7	chr2:86252000-86331200	Strong transcription	HUES64 Cell Line	embryonic stem cell
8	chr2:86252200-86282600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
9	chr2:86252200-86285200	Strong transcription	HUES48 Cell Line	embryonic stem cell
10	chr2:86252400-86283200	Strong transcription	H1 Cell Line	embryonic stem cell
11	chr2:86252600-86276800	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr2:86260600-86268800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
13	chr2:86260600-86269000	Enhancers	Primary T helper cells fromperipheralblood	blood
14	chr2:86260800-86268800	Weak transcription	Ovary	ovary
15	chr2:86261200-86272000	Strong transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr2:86263800-86268800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
17	chr2:86263800-86269200	Enhancers	Primary T cells fromperipheralblood	blood
18	chr2:86264000-86269000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr2:86264000-86281800	Strong transcription	Fetal Brain Female	brain
20	chr2:86264000-86332000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr2:86264200-86269600	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr2:86264200-86275400	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr2:86264400-86269000	Enhancers	Primary T helper cells PMA-I stimulated	--
24	chr2:86264400-86269800	Genic enhancers	Fetal Muscle Trunk	muscle
25	chr2:86264400-86279400	Strong transcription	Hela-S3	cervix
26	chr2:86264400-86285400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr2:86264400-86285400	Strong transcription	A549	lung
28	chr2:86264600-86273800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr2:86264800-86269800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
30	chr2:86264800-86273000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr2:86264800-86275400	Strong transcription	ES-I3 Cell Line	embryonic stem cell
32	chr2:86265000-86269800	Genic enhancers	Fetal Muscle Leg	muscle
33	chr2:86265200-86268800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
34	chr2:86265200-86268800	Genic enhancers	Dnd41	blood
35	chr2:86265200-86281600	Strong transcription	HMEC	breast
36	chr2:86265200-86284000	Strong transcription	NHEK	skin
37	chr2:86265200-86330000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr2:86265400-86269000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
39	chr2:86265400-86269200	Enhancers	Primary T helper naive cells from peripheral blood	blood
40	chr2:86265400-86282600	Strong transcription	Esophagus	oesophagus
41	chr2:86265400-86285200	Strong transcription	Fetal Intestine Large	intestine
42	chr2:86265400-86289800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr2:86265400-86289800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr2:86265600-86270200	Genic enhancers	Skeletal Muscle Female	skeletal muscle
45	chr2:86265600-86270200	Strong transcription	NH-A	brain
46	chr2:86265600-86272600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr2:86265600-86273200	Strong transcription	Aorta	Aorta
48	chr2:86265600-86274600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr2:86265600-86282000	Strong transcription	K562	blood
50	chr2:86265600-86282400	Strong transcription	Brain Germinal Matrix	brain

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