Variant report

Variant	rs7171983
Chromosome Location	chr15:31117842-31117843
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11070620	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11070624	0.86[AFR][1000 genomes]
rs11632454	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12439909	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1524878	0.81[AFR][1000 genomes]
rs2240101	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3829484	0.86[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs58844471	0.86[AFR][1000 genomes]
rs61260387	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs739831	0.86[AFR][1000 genomes]
rs757341	0.86[AFR][1000 genomes];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:23 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758374	chr15:30292944-31152491	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	59 gene(s)	inside rSNPs	diseases
2	esv2760022	chr15:30292944-31177476	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	61 gene(s)	inside rSNPs	diseases
3	nsv903757	chr15:30369153-31179534	Strong transcription Active TSS Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
4	nsv427955	chr15:30467980-31273174	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
5	nsv1052897	chr15:30501813-31184303	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
6	esv2757593	chr15:30605836-31177476	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers 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	41 gene(s)	inside rSNPs	diseases
7	nsv531138	chr15:30653877-31609679	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
8	nsv903822	chr15:30899133-31165955	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
9	nsv916936	chr15:30921917-31337510	Active TSS Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
10	nsv456744	chr15:30936285-31123235	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	nsv568761	chr15:30936285-31123235	Strong transcription Enhancers Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
12	nsv525795	chr15:30936285-31324531	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Flanking Active TSS 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 target site	35 gene(s)	inside rSNPs	diseases
13	nsv533434	chr15:30938215-31244225	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
14	nsv832950	chr15:30954625-31146464	Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
15	nsv1044683	chr15:30954725-31183908	Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
16	nsv542300	chr15:30954725-31183908	Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
17	nsv529701	chr15:30954726-31183907	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
18	nsv903831	chr15:30986051-31723279	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
19	nsv1046874	chr15:31008133-31294654	Enhancers Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
20	nsv1054147	chr15:31014507-31972706	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
21	nsv542306	chr15:31014507-31972706	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
22	nsv903833	chr15:31088443-31174687	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
23	nsv984044	chr15:31114428-31126547	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs7171983	RP11-540B6.2	cis	Whole Blood	GTEx
rs7171983	RP11-540B6.3	cis	lung	GTEx
rs7171983	FAN1	cis	Whole Blood	GTEx
rs7171983	RP11-540B6.2	cis	lung	GTEx
rs7171983	FAN1	cis	lung	GTEx
rs7171983	HERC2P10	cis	lung	GTEx

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:31110200-31118200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr15:31114400-31125000	Weak transcription	Pancreas	Pancrea
3	chr15:31116000-31120200	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr15:31116200-31118200	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr15:31116200-31120200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr15:31116200-31120600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr15:31116200-31125400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr15:31116200-31125400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr15:31116200-31125800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr15:31116200-31126200	Weak transcription	Brain Cingulate Gyrus	brain
11	chr15:31116200-31126600	Weak transcription	Brain Anterior Caudate	brain
12	chr15:31116200-31128000	Weak transcription	Fetal Brain Female	brain
13	chr15:31116200-31129800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr15:31116200-31131000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr15:31116200-31133600	Weak transcription	Osteobl	bone
16	chr15:31116200-31134200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr15:31116200-31135400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr15:31116200-31135400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr15:31116200-31136600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr15:31116400-31120200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr15:31116400-31125000	Weak transcription	Monocytes-CD14+_RO01746	blood
22	chr15:31116400-31126600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr15:31116400-31130600	Weak transcription	Placenta	Placenta
24	chr15:31116400-31135000	Weak transcription	Primary neutrophils fromperipheralblood	blood
25	chr15:31116600-31120200	Weak transcription	Hela-S3	cervix
26	chr15:31116800-31120000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr15:31117000-31120600	Weak transcription	HSMM	muscle
28	chr15:31117000-31124800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr15:31117000-31124800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr15:31117200-31120200	Weak transcription	Primary T helper cells PMA-I stimulated	--
31	chr15:31117200-31120600	Weak transcription	NH-A	brain
32	chr15:31117200-31125000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr15:31117200-31125200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr15:31117400-31118000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr15:31117400-31124600	Weak transcription	Spleen	Spleen
36	chr15:31117400-31125000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr15:31117400-31128800	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr15:31117600-31119000	Genic enhancers	Dnd41	blood
39	chr15:31117600-31120200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr15:31117600-31125000	Weak transcription	Primary T helper cells fromperipheralblood	blood

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