Variant report

Variant	rs16940260
Chromosome Location	chr16:75621073-75621074
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:75613643..75617035-chr16:75620700..75623039,3	MCF-7	breast:
2	chr16:75602647..75604231-chr16:75619831..75622343,2	MCF-7	breast:
3	chr16:75588871..75590659-chr16:75618802..75621133,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ADAT1-1	chr16:75616487-75622358	XLOC_012011

Variant related genes	Relation type
ENSG00000205084	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs11556641	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12922861	1.00[CEU][hapmap]
rs16940348	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16940362	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16940444	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16940961	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs16941287	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16941301	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16941409	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16941516	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16942032	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16975847	1.00[CHB][hapmap]
rs2164246	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2550320	1.00[AMR][1000 genomes]
rs2550889	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2550892	1.00[JPT][hapmap]
rs2550893	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs2550897	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2550900	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2550902	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs2550903	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2550905	0.80[EUR][1000 genomes]
rs2550906	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2550907	0.86[EUR][1000 genomes]
rs2550914	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2550915	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs2641803	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2641807	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2650406	0.86[EUR][1000 genomes]
rs2650410	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2650411	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2650413	1.00[JPT][hapmap]
rs2738800	1.00[AMR][1000 genomes]
rs55714466	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55862257	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56030666	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56321575	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs60919196	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7194333	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72563121	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73610805	0.86[EUR][1000 genomes]
rs74024796	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs74027409	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs74027420	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74027421	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74027424	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74027425	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74027427	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74027428	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74027431	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74027432	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74027433	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74027436	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74027439	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs74027441	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs74027443	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8192515	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs920037	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916502	chr16:74845880-75732365	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	131 gene(s)	inside rSNPs	diseases
2	nsv931939	chr16:75261354-75765025	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
3	nsv1065995	chr16:75373756-75626027	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	65 gene(s)	inside rSNPs	diseases
4	nsv525955	chr16:75473332-75628345	Strong transcription Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases
5	nsv532561	chr16:75519574-75636977	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
6	nsv532562	chr16:75614947-76371158	Weak transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription 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	50 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	chr16:75601200-75624400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr16:75604200-75622600	Weak transcription	Right Atrium	heart
3	chr16:75607000-75623200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr16:75607600-75630800	Weak transcription	Fetal Brain Male	brain
5	chr16:75609000-75627800	Weak transcription	NHEK	skin
6	chr16:75610400-75634000	Weak transcription	Hela-S3	cervix
7	chr16:75610600-75622800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr16:75610600-75622800	Weak transcription	Fetal Heart	heart
9	chr16:75610600-75633400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr16:75610600-75635200	Weak transcription	Fetal Kidney	kidney
11	chr16:75611000-75624800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr16:75611400-75622600	Weak transcription	Right Ventricle	heart
13	chr16:75611400-75634000	Weak transcription	Colonic Mucosa	Colon
14	chr16:75611800-75628800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr16:75612000-75622600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr16:75612000-75627400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr16:75612000-75627400	Weak transcription	Psoas Muscle	Psoas
18	chr16:75612000-75631000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr16:75612000-75635600	Weak transcription	Small Intestine	intestine
20	chr16:75612400-75624600	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr16:75612400-75631000	Weak transcription	Gastric	stomach
22	chr16:75612400-75631200	Weak transcription	Esophagus	oesophagus
23	chr16:75612600-75622200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr16:75613200-75622800	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr16:75613200-75622800	Weak transcription	Brain Germinal Matrix	brain
26	chr16:75613200-75624200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr16:75613200-75624400	Weak transcription	K562	blood
28	chr16:75613200-75624600	Weak transcription	Brain Cingulate Gyrus	brain
29	chr16:75613200-75624800	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr16:75613200-75624800	Weak transcription	NHLF	lung
31	chr16:75613200-75627200	Weak transcription	HepG2	liver
32	chr16:75613200-75627800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr16:75613200-75633400	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr16:75613400-75624400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr16:75613400-75624400	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr16:75613400-75624400	Weak transcription	HSMM	muscle
37	chr16:75613400-75624600	Weak transcription	NH-A	brain
38	chr16:75613400-75624800	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr16:75613400-75624800	Weak transcription	NHDF-Ad	bronchial
40	chr16:75613400-75630800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr16:75613400-75635200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
42	chr16:75613600-75622600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr16:75613600-75627400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr16:75613600-75630800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
45	chr16:75613600-75631000	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr16:75613600-75633000	Weak transcription	Ovary	ovary
47	chr16:75613800-75622800	Weak transcription	Stomach Smooth Muscle	stomach
48	chr16:75613800-75627400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr16:75613800-75627800	Weak transcription	A549	lung
50	chr16:75613800-75627800	Weak transcription	HUVEC	blood vessel

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