Variant report

Variant	rs16956707
Chromosome Location	chr15:31641633-31641634
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:31618069..31620740-chr15:31641222..31643035,2	K562	blood:

Variant related genes	Relation type
ENSG00000169926	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10438322	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs1075232	0.89[AMR][1000 genomes]
rs12437749	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12437800	1.00[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12437996	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs12438318	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12438813	0.91[AMR][1000 genomes]
rs12439239	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12439853	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1370062	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs16956738	0.94[AMR][1000 genomes]
rs1972825	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs34959140	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3743235	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs4450360	0.94[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs56396205	0.94[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs58156651	0.82[AMR][1000 genomes]
rs6493531	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs66501706	0.88[ASN][1000 genomes]
rs66581165	0.84[AMR][1000 genomes]
rs67634762	0.84[AMR][1000 genomes]
rs72722829	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72722847	0.94[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs72722861	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72724938	0.86[AMR][1000 genomes]
rs9672214	0.94[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs9672538	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	nsv932896	chr15:31292475-31730445	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Strong transcription 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	59 gene(s)	inside rSNPs	diseases
5	nsv903838	chr15:31452911-31672128	Strong transcription Flanking Active TSS Enhancers Genic enhancers Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
6	esv1815415	chr15:31483843-31697213	Genic enhancers Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
7	esv34100	chr15:31496514-31792591	Active TSS Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
8	nsv903840	chr15:31589970-31800149	Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
9	nsv1050482	chr15:31601016-31672921	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
10	nsv1048082	chr15:31610245-31667000	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
11	nsv1045944	chr15:31610245-31672921	Enhancers Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
12	nsv516681	chr15:31616674-31675453	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Active TSS 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	13 gene(s)	inside rSNPs	diseases
13	nsv903841	chr15:31616674-31697242	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
14	nsv903842	chr15:31621321-31697242	Weak transcription Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
15	nsv456748	chr15:31621321-31697642	Enhancers Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
16	nsv568801	chr15:31621321-31697642	Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
17	nsv1052942	chr15:31624164-31653633	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
18	esv1810782	chr15:31633161-31697642	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer 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	11 gene(s)	inside rSNPs	diseases
19	nsv1051910	chr15:31641254-31672921	Enhancers Strong transcription Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs16956707	CTD-3092A11.2	cis	Artery Tibial	GTEx
rs16956707	CTD-3092A11.2	cis	Whole Blood	GTEx
rs16956707	CHRNA7	cis	Artery Tibial	GTEx
rs16956707	RP11-932O9.9	cis	Esophagus Muscularis	GTEx
rs16956707	CHRNA7	cis	lung	GTEx
rs16956707	CHRNA7	cis	Whole Blood	GTEx
rs16956707	RP11-932O9.7	cis	lung	GTEx
rs16956707	GOLGA8R	cis	Heart Left Ventricle	GTEx
rs16956707	CTD-3092A11.2	cis	lung	GTEx
rs16956707	CHRNA7	cis	Thyroid	GTEx
rs16956707	RP11-932O9.7	cis	Artery Tibial	GTEx

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:31622800-31657400	Enhancers	Right Atrium	heart
2	chr15:31625200-31649000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr15:31627200-31643000	Genic enhancers	Spleen	Spleen
4	chr15:31631400-31644400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr15:31631400-31645000	Enhancers	Brain Substantia Nigra	brain
6	chr15:31631600-31644600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr15:31632200-31644400	Weak transcription	NH-A	brain
8	chr15:31634400-31644600	Enhancers	Brain Hippocampus Middle	brain
9	chr15:31635000-31644400	Weak transcription	Osteobl	bone
10	chr15:31635600-31644600	Weak transcription	Fetal Lung	lung
11	chr15:31637200-31643800	Weak transcription	HepG2	liver
12	chr15:31637400-31644800	Genic enhancers	Primary monocytes fromperipheralblood	blood
13	chr15:31637600-31643200	Genic enhancers	Gastric	stomach
14	chr15:31637600-31643800	Strong transcription	Fetal Stomach	stomach
15	chr15:31637800-31642600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr15:31637800-31642600	Weak transcription	HMEC	breast
17	chr15:31637800-31644400	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr15:31637800-31644600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr15:31638000-31642000	Strong transcription	Primary neutrophils fromperipheralblood	blood
20	chr15:31638000-31642000	Strong transcription	NHEK	skin
21	chr15:31638000-31643600	Weak transcription	NHLF	lung
22	chr15:31638000-31643800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr15:31638000-31644600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr15:31638000-31644800	Weak transcription	Hela-S3	cervix
25	chr15:31638200-31644600	Weak transcription	Aorta	Aorta
26	chr15:31638400-31643200	Genic enhancers	Fetal Muscle Trunk	muscle
27	chr15:31638400-31655400	Enhancers	Psoas Muscle	Psoas
28	chr15:31638600-31643000	Weak transcription	Rectal Smooth Muscle	rectum
29	chr15:31638800-31642000	Weak transcription	Fetal Heart	heart
30	chr15:31638800-31643400	Enhancers	Brain Angular Gyrus	brain
31	chr15:31639000-31641800	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
32	chr15:31639000-31642000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr15:31639000-31643000	Genic enhancers	Lung	lung
34	chr15:31639000-31646000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
35	chr15:31639400-31644800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr15:31639400-31644800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
37	chr15:31639600-31642600	Weak transcription	Brain Germinal Matrix	brain
38	chr15:31639600-31643600	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr15:31639600-31643600	Genic enhancers	Thymus	Thymus
40	chr15:31639600-31644600	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr15:31639600-31644600	Genic enhancers	Fetal Thymus	thymus
42	chr15:31639600-31644800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
43	chr15:31639800-31641800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr15:31639800-31645000	Genic enhancers	Primary B cells from peripheral blood	blood
45	chr15:31640000-31641800	Genic enhancers	Brain Inferior Temporal Lobe	brain
46	chr15:31640000-31643200	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
47	chr15:31640000-31643400	Genic enhancers	Primary T cells fromperipheralblood	blood
48	chr15:31640000-31643400	Genic enhancers	Rectal Mucosa Donor 29	rectum
49	chr15:31640000-31643800	Genic enhancers	Monocytes-CD14+_RO01746	blood
50	chr15:31640200-31641800	Genic enhancers	Brain Cingulate Gyrus	brain

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