Variant report

Variant	rs7220935
Chromosome Location	chr17:45703433-45703434
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:45700634..45703555-chr17:45708176..45711349,3	MCF-7	breast:
2	chr17:45700978..45703641-chr17:45726585..45728583,2	K562	blood:
3	chr17:45694079..45700174-chr17:45702807..45705612,6	K562	blood:
4	chr17:45694079..45699753-chr17:45702807..45705502,5	K562	blood:
5	chr17:45694884..45697521-chr17:45701270..45704059,2	MCF-7	breast:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AC040934.1-3	chr17:45703372-45703993	ENSG00000263766.1

No data

Variant related genes	Relation type
ENSG00000141279	Chromatin interaction
ENSG00000108424	Chromatin interaction
ENSG00000263766	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10163469	0.90[EUR][1000 genomes]
rs10853090	0.95[EUR][1000 genomes]
rs11079782	0.80[EUR][1000 genomes]
rs11079784	0.97[EUR][1000 genomes]
rs11650372	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11656855	0.95[EUR][1000 genomes]
rs11870935	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11871606	0.93[EUR][1000 genomes]
rs12150231	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12603290	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12937560	0.85[EUR][1000 genomes]
rs12943464	0.95[EUR][1000 genomes]
rs2317826	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35919601	0.81[EUR][1000 genomes]
rs3760370	0.96[EUR][1000 genomes]
rs3809868	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4092460	0.83[EUR][1000 genomes]
rs4239162	0.89[EUR][1000 genomes]
rs4239163	0.89[EUR][1000 genomes]
rs4264433	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4289035	0.96[EUR][1000 genomes]
rs4375701	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4399567	0.90[EUR][1000 genomes]
rs4580230	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4793842	0.91[EUR][1000 genomes]
rs4793908	0.93[EUR][1000 genomes]
rs4793913	0.92[EUR][1000 genomes]
rs4793978	0.97[EUR][1000 genomes]
rs4794001	0.95[EUR][1000 genomes]
rs4794016	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4794047	0.85[ASN][1000 genomes]
rs4794048	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55633793	0.91[EUR][1000 genomes]
rs56226803	0.92[EUR][1000 genomes]
rs62074014	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62074015	0.84[EUR][1000 genomes]
rs7207542	0.92[EUR][1000 genomes]
rs7210738	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7214799	0.82[EUR][1000 genomes]
rs7219303	0.92[EUR][1000 genomes]
rs7223029	0.96[EUR][1000 genomes]
rs73315878	0.90[EUR][1000 genomes]
rs8065437	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8065669	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8070759	0.81[EUR][1000 genomes]
rs8072100	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8075411	0.94[EUR][1000 genomes]
rs8077106	0.84[EUR][1000 genomes]
rs8078686	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8078880	0.94[EUR][1000 genomes]
rs8081717	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9891111	0.80[EUR][1000 genomes]
rs9905583	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9905922	0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062983	chr17:45030095-45789543	Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
2	nsv525267	chr17:45451894-45735706	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	esv1811231	chr17:45520374-45764956	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	esv1813964	chr17:45520374-45764956	Active TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	esv2758458	chr17:45520374-45764956	Weak transcription Transcr. at gene 5' and 3' Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
6	esv2758693	chr17:45520374-45764956	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
7	nsv428344	chr17:45520374-45764956	Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7220935	MRPL45P2	cis	Skin Sun Exposed Lower leg	GTEx
rs7220935	TBKBP1	cis	Nerve Tibial	GTEx
rs7220935	TBKBP1	cis	Artery Tibial	GTEx
rs7220935	KPNB1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45667400-45718200	Strong transcription	Primary neutrophils fromperipheralblood	blood
2	chr17:45672400-45704200	Strong transcription	Fetal Muscle Trunk	muscle
3	chr17:45689200-45707800	Weak transcription	Gastric	stomach
4	chr17:45691800-45716600	Weak transcription	Right Ventricle	heart
5	chr17:45692800-45714600	Weak transcription	Aorta	Aorta
6	chr17:45695400-45704000	Strong transcription	GM12878-XiMat	blood
7	chr17:45696600-45709200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr17:45696600-45713600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr17:45696600-45726000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr17:45696800-45707200	Weak transcription	Ovary	ovary
11	chr17:45696800-45726200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr17:45697000-45725800	Weak transcription	Brain Substantia Nigra	brain
13	chr17:45697200-45703600	Weak transcription	Fetal Brain Male	brain
14	chr17:45697200-45713400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr17:45697200-45713600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr17:45697200-45726000	Weak transcription	Brain Angular Gyrus	brain
17	chr17:45698000-45716000	Weak transcription	Psoas Muscle	Psoas
18	chr17:45698600-45714400	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr17:45699400-45707200	Weak transcription	Pancreas	Pancrea
20	chr17:45699400-45707200	Weak transcription	Right Atrium	heart
21	chr17:45699400-45726000	Weak transcription	Brain Anterior Caudate	brain
22	chr17:45699400-45726200	Weak transcription	Fetal Kidney	kidney
23	chr17:45699600-45713800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr17:45699800-45707200	Weak transcription	Stomach Mucosa	stomach
25	chr17:45699800-45707800	Weak transcription	K562	blood
26	chr17:45699800-45712600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr17:45699800-45713400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr17:45699800-45717600	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr17:45700000-45704200	Strong transcription	Fetal Muscle Leg	muscle
30	chr17:45700000-45707200	Weak transcription	Fetal Lung	lung
31	chr17:45700000-45710000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr17:45700000-45714000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr17:45700000-45725600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr17:45700000-45725800	Weak transcription	Spleen	Spleen
35	chr17:45700200-45707400	Weak transcription	Fetal Heart	heart
36	chr17:45700200-45708000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr17:45700200-45713000	Weak transcription	Brain Germinal Matrix	brain
38	chr17:45700400-45703800	Weak transcription	Small Intestine	intestine
39	chr17:45700400-45704200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
40	chr17:45700400-45725800	Weak transcription	Primary B cells from peripheral blood	blood
41	chr17:45700600-45703600	Weak transcription	Rectal Smooth Muscle	rectum
42	chr17:45700600-45725200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr17:45701200-45704000	Strong transcription	Osteobl	bone
44	chr17:45701200-45711600	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr17:45701200-45713000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr17:45701400-45703600	Weak transcription	Colon Smooth Muscle	Colon
47	chr17:45701400-45703800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr17:45701400-45703800	Weak transcription	Dnd41	blood
49	chr17:45701400-45703800	Weak transcription	NH-A	brain
50	chr17:45701400-45704200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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