Variant report

Variant	rs16906634
Chromosome Location	chr10:52371915-52371916
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:52359176..52362800-chr10:52370214..52372763,3	K562	blood:
2	chr10:52321910..52324715-chr10:52371827..52374232,3	K562	blood:
3	chr10:52371729..52375098-chr10:52383274..52385073,4	MCF-7	breast:
4	chr10:52359953..52362709-chr10:52369369..52373300,4	MCF-7	breast:
5	chr10:52371171..52374113-chr10:52380759..52382982,2	MCF-7	breast:
6	chr10:52359176..52361319-chr10:52370214..52372763,2	K562	blood:
7	chr10:52367499..52369355-chr10:52371590..52373670,2	MCF-7	breast:
8	chr10:52363840..52365627-chr10:52371839..52373893,2	K562	blood:
9	chr10:52366580..52370875-chr10:52371309..52374318,4	K562	blood:
10	chr10:52367316..52369194-chr10:52370537..52372396,2	MCF-7	breast:
11	chr10:52371856..52377048-chr10:52377440..52385994,18	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000198964	Chromatin interaction
ENSG00000226200	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10160082	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11006407	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11006510	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11006513	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11006527	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12247712	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12247977	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12248247	0.82[AFR][1000 genomes]
rs12248669	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12248873	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12249902	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12250028	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12260665	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12260996	0.90[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12261261	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12265805	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9919374	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9919407	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1054775	chr10:51595893-52392361	Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv1051087	chr10:51886486-52447295	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv916214	chr10:51886486-52458983	Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv918212	chr10:51886486-52465482	Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv817412	chr10:51911034-52432990	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
6	nsv469522	chr10:52276564-52447589	Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
7	nsv482564	chr10:52276564-52447589	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16906634	NAP1L2	trans	lymphoblastoid	seeQTL

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:52341200-52373000	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr10:52360200-52375600	Enhancers	Skeletal Muscle Female	skeletal muscle
3	chr10:52362200-52372400	Weak transcription	Esophagus	oesophagus
4	chr10:52363200-52372000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr10:52364400-52372000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
6	chr10:52364400-52374400	Weak transcription	Primary B cells from peripheral blood	blood
7	chr10:52365200-52374000	Weak transcription	Placenta	Placenta
8	chr10:52365400-52375000	Weak transcription	Fetal Brain Female	brain
9	chr10:52365400-52379400	Weak transcription	Primary hematopoietic stem cells	blood
10	chr10:52365600-52372000	Weak transcription	Fetal Kidney	kidney
11	chr10:52365600-52377200	Weak transcription	Primary T cells from cord blood	blood
12	chr10:52365800-52372400	Weak transcription	Fetal Intestine Small	intestine
13	chr10:52365800-52378200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr10:52366000-52373000	Weak transcription	Fetal Intestine Large	intestine
15	chr10:52366000-52381600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr10:52366600-52372600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr10:52366600-52377800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr10:52367200-52377800	Weak transcription	Primary B cells from cord blood	blood
19	chr10:52367200-52379400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr10:52367400-52381400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr10:52367600-52372000	Weak transcription	GM12878-XiMat	blood
22	chr10:52367600-52372800	Weak transcription	NHDF-Ad	bronchial
23	chr10:52367600-52378400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr10:52367600-52381400	Weak transcription	NHLF	lung
25	chr10:52367600-52381400	Weak transcription	Osteobl	bone
26	chr10:52368000-52372600	Weak transcription	HepG2	liver
27	chr10:52368000-52374200	Weak transcription	Stomach Mucosa	stomach
28	chr10:52368200-52373400	Enhancers	Fetal Muscle Leg	muscle
29	chr10:52368200-52375400	Enhancers	Pancreas	Pancrea
30	chr10:52368400-52372400	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr10:52368800-52372800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr10:52369000-52378800	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr10:52369200-52372600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr10:52369200-52375800	Enhancers	Fetal Heart	heart
35	chr10:52369400-52372400	Enhancers	Ovary	ovary
36	chr10:52369400-52375400	Enhancers	Brain Anterior Caudate	brain
37	chr10:52369600-52374200	Enhancers	Fetal Lung	lung
38	chr10:52369600-52374800	Enhancers	Brain Cingulate Gyrus	brain
39	chr10:52369600-52375400	Enhancers	Psoas Muscle	Psoas
40	chr10:52369600-52375400	Enhancers	Skeletal Muscle Male	skeletal muscle
41	chr10:52369600-52375800	Enhancers	Brain Angular Gyrus	brain
42	chr10:52369600-52375800	Enhancers	Brain Hippocampus Middle	brain
43	chr10:52369800-52373000	Enhancers	Brain Inferior Temporal Lobe	brain
44	chr10:52369800-52374400	Enhancers	Brain Substantia Nigra	brain
45	chr10:52369800-52376200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
46	chr10:52370000-52372400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr10:52370200-52373600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr10:52370200-52378400	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr10:52370600-52372200	Enhancers	Primary T helper cells PMA-I stimulated	--
50	chr10:52370600-52372800	Weak transcription	Fetal Thymus	thymus

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