Variant report

Variant	rs6598679
Chromosome Location	chr16:46655210-46655211
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:46651769..46655217-chr16:46661271..46664188,4	K562	blood:
2	chr16:46649901..46653063-chr16:46653348..46656157,4	K562	blood:
3	chr16:46653721..46656886-chr16:46721851..46724551,4	K562	blood:
4	chr16:46589331..46591714-chr16:46654314..46656100,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-VPS35-1	chr16:46655169-46655263	NONHSAT142254

Variant related genes	Relation type
ENSG00000171241	Chromatin interaction
ENSG00000091651	Chromatin interaction
ENSG00000199448	Chromatin interaction
ENSG00000069329	Chromatin interaction

Extended variants
information (count: 127 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:106)

rs_ID	r²[population]
rs10902629	1.00[AMR][1000 genomes]
rs11860636	0.87[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12598707	1.00[AMR][1000 genomes]
rs1436435	1.00[YRI][hapmap]
rs1530895	1.00[AMR][1000 genomes]
rs1641120	1.00[AMR][1000 genomes]
rs1645939	1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1651658	1.00[AMR][1000 genomes]
rs1651659	1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs166096	1.00[AMR][1000 genomes]
rs168745	1.00[AMR][1000 genomes]
rs1698957	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs185213	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs1865837	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1865838	1.00[AMR][1000 genomes]
rs194054	1.00[AMR][1000 genomes]
rs194055	1.00[AMR][1000 genomes]
rs1992075	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1992078	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2011677	0.85[AFR][1000 genomes]
rs2033673	1.00[AMR][1000 genomes]
rs2164516	1.00[AFR][1000 genomes]
rs2334116	1.00[YRI][hapmap]
rs250420	1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs250421	1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs252723	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs252724	1.00[AMR][1000 genomes]
rs252725	1.00[AMR][1000 genomes]
rs252727	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs252728	1.00[AMR][1000 genomes]
rs252732	1.00[AMR][1000 genomes]
rs252733	1.00[AMR][1000 genomes]
rs252734	1.00[AMR][1000 genomes]
rs28185	1.00[AMR][1000 genomes]
rs36309	1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs36311	1.00[AMR][1000 genomes]
rs36313	1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs36314	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs36317	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs36459	1.00[AMR][1000 genomes]
rs36460	1.00[YRI][hapmap]
rs36461	1.00[AMR][1000 genomes]
rs36463	1.00[AMR][1000 genomes]
rs36465	1.00[AMR][1000 genomes]
rs36466	1.00[AMR][1000 genomes]
rs36467	1.00[AMR][1000 genomes]
rs36470	1.00[AMR][1000 genomes]
rs36473	1.00[AMR][1000 genomes]
rs36474	1.00[AMR][1000 genomes]
rs36475	1.00[AMR][1000 genomes]
rs36477	1.00[AMR][1000 genomes]
rs36480	1.00[YRI][hapmap]
rs36482	1.00[AMR][1000 genomes]
rs396907	1.00[YRI][hapmap]
rs40164	1.00[AMR][1000 genomes]
rs408906	1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs41232	1.00[AMR][1000 genomes]
rs414928	1.00[AMR][1000 genomes]
rs420560	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs425556	1.00[AMR][1000 genomes]
rs438275	1.00[AMR][1000 genomes]
rs449778	1.00[AMR][1000 genomes]
rs4640213	1.00[YRI][hapmap]
rs4966488	1.00[YRI][hapmap]
rs4966571	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4966603	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4967248	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4967259	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4967594	1.00[AMR][1000 genomes]
rs4967595	1.00[AMR][1000 genomes]
rs62057622	1.00[AMR][1000 genomes]
rs633699	1.00[AMR][1000 genomes]
rs637583	1.00[AMR][1000 genomes]
rs6598600	1.00[YRI][hapmap]
rs6598601	1.00[YRI][hapmap]
rs6598661	1.00[AMR][1000 genomes]
rs695997	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs698417	1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs698419	1.00[AMR][1000 genomes]
rs700580	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs700581	1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7187176	1.00[YRI][hapmap]
rs7198683	1.00[AMR][1000 genomes]
rs7206393	1.00[AMR][1000 genomes]
rs794283	1.00[AMR][1000 genomes]
rs794557	1.00[AMR][1000 genomes]
rs794558	1.00[AMR][1000 genomes]
rs794559	1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs797016	1.00[AMR][1000 genomes]
rs8044120	1.00[AMR][1000 genomes]
rs8046818	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs8047302	1.00[AMR][1000 genomes]
rs8048535	1.00[AMR][1000 genomes]
rs8049734	1.00[AMR][1000 genomes]
rs8059285	1.00[AMR][1000 genomes]
rs808078	1.00[YRI][hapmap]
rs808428	1.00[AMR][1000 genomes]
rs808436	1.00[AMR][1000 genomes]
rs811196	0.87[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs811267	1.00[AMR][1000 genomes]
rs811734	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs937659	1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9922581	1.00[AMR][1000 genomes]
rs9924386	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9925083	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9935045	1.00[YRI][hapmap];1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1799780	chr16:46386457-46875496	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	esv1848852	chr16:46463746-46659554	Strong transcription Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv917899	chr16:46463769-46669332	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv1056162	chr16:46463770-46655516	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv1066221	chr16:46463770-46699143	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
6	nsv1060734	chr16:46463770-46768102	Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
7	nsv1064289	chr16:46463770-46801977	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
8	nsv1059456	chr16:46463770-47307580	Flanking Active TSS Bivalent/Poised TSS Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
9	nsv1066115	chr16:46463770-47318415	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
10	esv1806429	chr16:46468179-46659554	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
11	esv1847767	chr16:46474763-46659354	Bivalent Enhancer Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
12	esv1815153	chr16:46474763-46672206	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats 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	11 gene(s)	inside rSNPs	diseases
13	esv1797185	chr16:46489836-46731413	Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
14	nsv1066048	chr16:46500740-46998694	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
15	nsv542908	chr16:46500740-46998694	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
16	nsv1059147	chr16:46500740-47010960	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers 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	54 gene(s)	inside rSNPs	diseases
17	nsv542909	chr16:46500740-47010960	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
18	nsv833216	chr16:46501297-46671860	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
19	nsv916976	chr16:46505597-46801868	Active TSS Bivalent Enhancer Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
20	nsv526656	chr16:46539392-46846663	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
21	nsv428327	chr16:46556968-46718490	Enhancers Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:46653600-46655600	Active TSS	GM12878-XiMat	blood
2	chr16:46654000-46655400	Active TSS	Rectal Mucosa Donor 29	rectum
3	chr16:46654000-46655400	Active TSS	NH-A	brain
4	chr16:46654000-46655600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr16:46654000-46655600	Active TSS	HUES6 Cell Line	embryonic stem cell
6	chr16:46654000-46655600	Active TSS	iPS-20b Cell Line	embryonic stem cell
7	chr16:46654000-46655600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr16:46654000-46655600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr16:46654000-46655600	Active TSS	A549	lung
10	chr16:46654000-46655600	Active TSS	NHDF-Ad	bronchial
11	chr16:46654000-46655800	Active TSS	ES-I3 Cell Line	embryonic stem cell
12	chr16:46654200-46655400	Active TSS	HSMM	muscle
13	chr16:46654200-46655600	Active TSS	H1 Cell Line	embryonic stem cell
14	chr16:46654200-46655600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr16:46654200-46655600	Active TSS	iPS-18 Cell Line	embryonic stem cell
16	chr16:46654200-46655600	Flanking Active TSS	Primary hematopoietic stem cells	blood
17	chr16:46654200-46655800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
18	chr16:46654400-46655400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr16:46654400-46655400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr16:46654400-46655400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr16:46654400-46655400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
22	chr16:46654400-46655400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr16:46654400-46655400	Active TSS	Fetal Kidney	kidney
24	chr16:46654400-46655600	Active TSS	HUES48 Cell Line	embryonic stem cell
25	chr16:46654400-46655600	Active TSS	iPS-15b Cell Line	embryonic stem cell
26	chr16:46654400-46655600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr16:46654400-46655600	Active TSS	Brain Substantia Nigra	brain
28	chr16:46654400-46655600	Active TSS	Hela-S3	cervix
29	chr16:46654400-46655800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
30	chr16:46654400-46655800	Active TSS	Rectal Smooth Muscle	rectum
31	chr16:46654600-46655400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr16:46654600-46655400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr16:46654600-46655400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr16:46654600-46655400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr16:46654600-46655400	Active TSS	Primary T cells from cord blood	blood
36	chr16:46654600-46655400	Active TSS	Brain Anterior Caudate	brain
37	chr16:46654600-46655400	Active TSS	Pancreatic Islets	Pancreatic Islet
38	chr16:46654600-46655400	Active TSS	Dnd41	blood
39	chr16:46654600-46655400	Active TSS	HUVEC	blood vessel
40	chr16:46654600-46655400	Active TSS	K562	blood
41	chr16:46654600-46655400	Active TSS	NHLF	lung
42	chr16:46654600-46655400	Active TSS	Osteobl	bone
43	chr16:46654600-46655600	Active TSS	H9 Cell Line	embryonic stem cell
44	chr16:46654600-46655600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr16:46654600-46655600	Active TSS	HUES64 Cell Line	embryonic stem cell
46	chr16:46654600-46655600	Active TSS	Muscle Satellite Cultured Cells	--
47	chr16:46654600-46655600	Active TSS	Fetal Intestine Small	intestine
48	chr16:46654600-46655600	Flanking Active TSS	Placenta	Placenta
49	chr16:46654600-46655600	Active TSS	Ovary	ovary
50	chr16:46654600-46655600	Active TSS	Placenta Amnion	Placenta Amnion

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