Variant report

Variant	rs16897900
Chromosome Location	chr6:30755893-30755894
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:30705811..30713504-chr6:30753060..30768565,33	MCF-7	breast:
2	chr6:30749730..30752647-chr6:30754925..30756551,2	MCF-7	breast:
3	chr6:30754150..30756442-chr6:30758530..30761272,2	K562	blood:
4	chr6:30748336..30749911-chr6:30753727..30756434,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000137312	Chromatin interaction
ENSG00000228022	Chromatin interaction
ENSG00000272273	Chromatin interaction
ENSG00000137331	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10947091	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10947095	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11758688	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12526481	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12527415	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12527745	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13196596	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13197105	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13197117	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13197227	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13201769	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13201901	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13206009	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13207758	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13210146	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13211218	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13213720	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16897899	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28780116	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28780119	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28894083	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28894084	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28894085	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28894089	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3131042	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs3131043	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs3131046	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs3131051	0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4711228	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4711229	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4713360	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4713362	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4713365	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4713366	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4713367	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4713368	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6900029	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6920124	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7740474	0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7740525	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9295912	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9295914	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9461630	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9461631	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9468830	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9468832	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9468833	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3519970	chr6:30382942-31378788	Genic enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
2	esv3519971	chr6:30382942-31378788	Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
3	nsv601481	chr6:30422632-31284253	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1012 gene(s)	inside rSNPs	diseases
4	esv3430377	chr6:30443802-30814426	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	967 gene(s)	inside rSNPs	diseases
5	esv2758041	chr6:30644693-30816319	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	223 gene(s)	inside rSNPs	diseases
6	esv2759413	chr6:30644693-30816319	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	223 gene(s)	inside rSNPs	diseases
7	nsv1015372	chr6:30704734-31582152	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
8	nsv538173	chr6:30704734-31582152	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
9	nsv527226	chr6:30716719-30772378	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
10	nsv1023695	chr6:30754540-30773349	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
11	esv16033	chr6:30755746-30756386	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16897900	NKAPL	cis	cerebellum	SCAN

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30744000-30758000	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr6:30749400-30761200	Weak transcription	Lung	lung
3	chr6:30749800-30757000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr6:30750000-30756000	Enhancers	Primary neutrophils fromperipheralblood	blood
5	chr6:30750400-30761200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr6:30750600-30756000	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr6:30750600-30756000	Weak transcription	Stomach Mucosa	stomach
8	chr6:30750600-30758000	Weak transcription	Fetal Heart	heart
9	chr6:30750800-30761200	Weak transcription	Small Intestine	intestine
10	chr6:30750800-30761600	Weak transcription	NHDF-Ad	bronchial
11	chr6:30751000-30756000	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr6:30751000-30756000	Weak transcription	HMEC	breast
13	chr6:30751000-30769800	Weak transcription	Right Ventricle	heart
14	chr6:30751200-30756600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr6:30751200-30757800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr6:30752200-30756000	Weak transcription	Duodenum Mucosa	Duodenum
17	chr6:30753000-30758000	Enhancers	Dnd41	blood
18	chr6:30753400-30757200	Enhancers	HepG2	liver
19	chr6:30753800-30757600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
20	chr6:30754200-30756800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
21	chr6:30754600-30756000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr6:30754600-30756400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr6:30754600-30761400	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr6:30754800-30756000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr6:30754800-30756000	Weak transcription	Osteobl	bone
26	chr6:30755000-30756000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr6:30755000-30756000	Weak transcription	K562	blood
28	chr6:30755400-30757600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr6:30755600-30756000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr6:30755600-30756000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr6:30755600-30756200	Enhancers	NH-A	brain
32	chr6:30755600-30756400	Enhancers	A549	lung
33	chr6:30755600-30756600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
34	chr6:30755600-30756800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
35	chr6:30755600-30757000	Enhancers	Primary T killer memory cells from peripheral blood	blood
36	chr6:30755600-30757400	Enhancers	Primary T helper cells fromperipheralblood	blood
37	chr6:30755600-30757600	Enhancers	Hela-S3	cervix
38	chr6:30755600-30757800	Enhancers	Primary T helper cells PMA-I stimulated	--
39	chr6:30755600-30758000	Enhancers	Primary T cells from cord blood	blood
40	chr6:30755800-30756000	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
41	chr6:30755800-30756000	Enhancers	Adipose Nuclei	Adipose
42	chr6:30755800-30756200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
43	chr6:30755800-30756200	Enhancers	Right Atrium	heart
44	chr6:30755800-30756200	Enhancers	Stomach Smooth Muscle	stomach
45	chr6:30755800-30756200	Enhancers	GM12878-XiMat	blood
46	chr6:30755800-30756400	Enhancers	Placenta	Placenta
47	chr6:30755800-30756600	Enhancers	Primary B cells from cord blood	blood
48	chr6:30755800-30756600	Enhancers	Colon Smooth Muscle	Colon
49	chr6:30755800-30756600	Enhancers	Rectal Smooth Muscle	rectum
50	chr6:30755800-30756800	Enhancers	Primary T helper naive cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links