Variant report

Variant	rs16961564
Chromosome Location	chr17:17232242-17232243
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:17228475..17230243-chr17:17230448..17232701,2	K562	blood:
2	chr17:17208563..17211113-chr17:17230202..17232936,2	K562	blood:

Extended variants
information (count: 16 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs11867932	1.00[CHB][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs171394	0.80[EUR][1000 genomes]
rs242242	0.80[EUR][1000 genomes]
rs242244	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833380	chr17:17088416-17241206	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv833382	chr17:17124329-17305683	Genic enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv469777	chr17:17127385-17272698	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv482546	chr17:17127385-17272698	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv1061186	chr17:17200427-17314406	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
6	esv3321712	chr17:17228427-17233225	Weak transcription Strong transcription Enhancers Genic enhancers Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	esv3347241	chr17:17229227-17232425	Weak transcription Genic enhancers Strong transcription Enhancers Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	esv3324358	chr17:17229452-17232600	Strong transcription Genic enhancers Weak transcription Enhancers Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	esv3377670	chr17:17229677-17232275	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	esv10397	chr17:17231284-17235583	Weak transcription Strong transcription Enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	nsv978337	chr17:17231433-17235881	Weak transcription Enhancers Strong transcription Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	nsv960382	chr17:17231433-17252299	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs16961564	ZNF287	cis	cerebellum	SCAN
rs16961564	SLC47A2	cis	cerebellum	SCAN
rs16961564	PRPSAP2	cis	cerebellum	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:17207400-17235400	Weak transcription	Lung	lung
2	chr17:17207600-17246400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr17:17207800-17243400	Weak transcription	Colon Smooth Muscle	Colon
4	chr17:17208600-17255400	Weak transcription	Brain Substantia Nigra	brain
5	chr17:17208800-17236000	Weak transcription	Right Ventricle	heart
6	chr17:17210600-17233400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr17:17213000-17248000	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr17:17215600-17252800	Weak transcription	Fetal Lung	lung
9	chr17:17216600-17240800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr17:17217200-17253800	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr17:17218600-17239800	Weak transcription	Fetal Thymus	thymus
12	chr17:17219000-17255400	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr17:17224600-17248200	Weak transcription	Pancreas	Pancrea
14	chr17:17226000-17235600	Weak transcription	Spleen	Spleen
15	chr17:17226600-17251200	Weak transcription	Primary T cells from cord blood	blood
16	chr17:17226800-17246800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr17:17227200-17254000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr17:17228200-17258200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr17:17228600-17255000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr17:17228800-17245600	Weak transcription	Brain Cingulate Gyrus	brain
21	chr17:17229000-17245800	Weak transcription	Dnd41	blood
22	chr17:17229200-17247400	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr17:17229200-17255200	Weak transcription	Brain Hippocampus Middle	brain
24	chr17:17229400-17247800	Weak transcription	Fetal Intestine Small	intestine
25	chr17:17229600-17245600	Weak transcription	Brain Angular Gyrus	brain
26	chr17:17229600-17246000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr17:17229800-17258400	Weak transcription	Thymus	Thymus
28	chr17:17230000-17245800	Weak transcription	Brain Germinal Matrix	brain
29	chr17:17230000-17246400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr17:17230000-17250000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr17:17230200-17232400	Weak transcription	Gastric	stomach
32	chr17:17230200-17235400	Weak transcription	Fetal Stomach	stomach
33	chr17:17230200-17236600	Weak transcription	Ovary	ovary
34	chr17:17230200-17245400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr17:17230200-17245400	Weak transcription	Fetal Muscle Leg	muscle
36	chr17:17230200-17246000	Weak transcription	Fetal Muscle Trunk	muscle
37	chr17:17230200-17250600	Weak transcription	Adipose Nuclei	Adipose
38	chr17:17230200-17252200	Weak transcription	Stomach Smooth Muscle	stomach
39	chr17:17230200-17258200	Weak transcription	Brain Anterior Caudate	brain
40	chr17:17231600-17232800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
41	chr17:17231600-17247800	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr17:17232000-17244600	Weak transcription	Primary hematopoietic stem cells	blood
43	chr17:17232200-17244800	Weak transcription	Fetal Brain Female	brain

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