Variant report

Variant	rs4968305
Chromosome Location	chr17:45158283-45158284
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:45155821..45158287-chr17:45163734..45167832,3	K562	blood:
2	chr17:45156502..45159050-chr17:45162212..45165184,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RPRML-3	chr17:45158273-45158298	NONHSAT054279

Extended variants
information (count: 29 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs12450537	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1630431	0.82[YRI][hapmap];1.00[ASN][1000 genomes]
rs1634272	0.86[ASN][1000 genomes]
rs2004580	0.91[CEU][hapmap];1.00[CHB][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2316667	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4061304	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4387650	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4520895	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58675395	0.86[ASN][1000 genomes]
rs62074463	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8064557	1.00[ASN][1000 genomes]
rs8073829	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9894300	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9897338	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9911627	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3492820	chr17:44174959-45161556	Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	esv3492821	chr17:44174959-45161556	Weak transcription Genic enhancers Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
3	esv3502492	chr17:44305975-45169159	Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
4	esv3502493	chr17:44305975-45169159	Active TSS Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
5	nsv833466	chr17:45020360-45204537	Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	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
7	nsv833467	chr17:45063935-45252624	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
8	nsv522797	chr17:45084279-45183152	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
9	esv3332795	chr17:45116212-45209297	Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers 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	13 gene(s)	inside rSNPs	diseases
10	esv3386521	chr17:45116232-45209267	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
11	esv21010	chr17:45125753-45177221	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
12	nsv1059766	chr17:45130765-45203468	Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
13	esv2760450	chr17:45130777-45225222	Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
14	nsv521632	chr17:45151549-45196190	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4968305	RP11-156P1.3	cis	lung	GTEx
rs4968305	RP11-156P1.3	cis	Whole Blood	GTEx
rs4968305	RP11-156P1.3	cis	Esophagus Mucosa	GTEx

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45145000-45158800	Weak transcription	NHLF	lung
2	chr17:45145000-45163600	Weak transcription	Aorta	Aorta
3	chr17:45145000-45163800	Weak transcription	Small Intestine	intestine
4	chr17:45145000-45164600	Weak transcription	Brain Angular Gyrus	brain
5	chr17:45145000-45169800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr17:45145000-45169800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr17:45145000-45169800	Weak transcription	Fetal Lung	lung
8	chr17:45145000-45176400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr17:45145000-45176600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr17:45145000-45176800	Weak transcription	Lung	lung
11	chr17:45145200-45158800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr17:45145200-45162200	Weak transcription	HepG2	liver
13	chr17:45145200-45169200	Weak transcription	Primary B cells from cord blood	blood
14	chr17:45145200-45170200	Weak transcription	Brain Germinal Matrix	brain
15	chr17:45145200-45176600	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr17:45145400-45176000	Weak transcription	Primary T cells from cord blood	blood
17	chr17:45146000-45158600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr17:45146400-45169800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr17:45146400-45170800	Weak transcription	Dnd41	blood
20	chr17:45148600-45162200	Weak transcription	Stomach Mucosa	stomach
21	chr17:45148800-45161200	Weak transcription	Hela-S3	cervix
22	chr17:45148800-45175400	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr17:45149000-45164200	Weak transcription	Primary T helper cells fromperipheralblood	blood
24	chr17:45149000-45168600	Weak transcription	Primary B cells from peripheral blood	blood
25	chr17:45149000-45170000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr17:45149000-45173800	Weak transcription	Primary T helper cells PMA-I stimulated	--
27	chr17:45149600-45175400	Weak transcription	Primary T cells fromperipheralblood	blood
28	chr17:45149600-45176800	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr17:45150200-45170000	Weak transcription	Ovary	ovary
30	chr17:45150200-45174600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr17:45150600-45159200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr17:45150600-45162400	Weak transcription	K562	blood
33	chr17:45150600-45162800	Weak transcription	Primary hematopoietic stem cells	blood
34	chr17:45150600-45163000	Weak transcription	GM12878-XiMat	blood
35	chr17:45150600-45164600	Weak transcription	Brain Anterior Caudate	brain
36	chr17:45150600-45167200	Weak transcription	Spleen	Spleen
37	chr17:45150600-45169800	Weak transcription	Fetal Muscle Leg	muscle
38	chr17:45150600-45170600	Weak transcription	HSMM	muscle
39	chr17:45150600-45176400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr17:45150600-45176800	Weak transcription	Left Ventricle	heart
41	chr17:45150800-45161600	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr17:45152800-45159600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr17:45153600-45161400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr17:45155000-45169800	Weak transcription	Fetal Brain Female	brain
45	chr17:45155600-45159000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr17:45155600-45162800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr17:45155600-45170200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr17:45155600-45170200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr17:45155600-45170200	Weak transcription	NHEK	skin
50	chr17:45155600-45173600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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