Variant report

Variant	rs16846839
Chromosome Location	chr1:227215967-227215968
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:227210940..227212945-chr1:227215048..227216859,2	K562	blood:

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs12562621	0.89[CHB][hapmap]
rs12562646	0.89[CHB][hapmap]
rs12565212	0.89[CHB][hapmap];1.00[GIH][hapmap]
rs12565685	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[ASN][1000 genomes]
rs16841298	0.89[CHB][hapmap];1.00[GIH][hapmap]
rs16846738	0.86[CHB][hapmap]
rs16846751	0.89[CHB][hapmap]
rs16846772	0.89[CHB][hapmap];1.00[GIH][hapmap]
rs16846783	0.89[CHB][hapmap];1.00[GIH][hapmap]
rs16846798	0.89[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap]
rs16846903	1.00[CHB][hapmap]
rs16846944	1.00[CHB][hapmap]
rs16847001	1.00[CHB][hapmap]
rs16847020	1.00[CHB][hapmap]
rs2297411	0.89[CHB][hapmap];1.00[GIH][hapmap]
rs3795452	0.89[CHB][hapmap];1.00[GIH][hapmap]
rs41527149	0.89[CHB][hapmap];1.00[GIH][hapmap]
rs961490	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003656	chr1:227034700-227559665	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv535318	chr1:227034700-227559665	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv1005811	chr1:227196502-227215967	Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv1007352	chr1:227196502-227247160	ZNF genes & repeats Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv997751	chr1:227196502-227263537	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv1011654	chr1:227196502-227308416	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv1010864	chr1:227199493-227246753	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv1014423	chr1:227201253-227268843	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv832792	chr1:227211378-227364992	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv1012482	chr1:227212024-227271750	Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16846839	CDC42BPA	cis	lymphoblastoid	seeQTL

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227154400-227294200	Weak transcription	Hela-S3	cervix
2	chr1:227175600-227216200	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr1:227176000-227216400	Weak transcription	NHLF	lung
4	chr1:227177400-227255200	Weak transcription	Small Intestine	intestine
5	chr1:227178400-227271200	Weak transcription	Psoas Muscle	Psoas
6	chr1:227178600-227226200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr1:227182000-227216000	Weak transcription	Colon Smooth Muscle	Colon
8	chr1:227182800-227224200	Weak transcription	Spleen	Spleen
9	chr1:227183200-227228200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr1:227183200-227240400	Weak transcription	Colonic Mucosa	Colon
11	chr1:227184000-227234000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr1:227187200-227218600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr1:227190600-227217000	Weak transcription	Esophagus	oesophagus
14	chr1:227190600-227223200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr1:227190600-227272600	Weak transcription	Lung	lung
16	chr1:227192600-227220200	Weak transcription	Rectal Smooth Muscle	rectum
17	chr1:227192800-227220200	Weak transcription	Gastric	stomach
18	chr1:227202600-227217200	Strong transcription	Adipose Nuclei	Adipose
19	chr1:227202600-227222600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr1:227203000-227278800	Weak transcription	Pancreas	Pancrea
21	chr1:227205400-227216400	Weak transcription	HepG2	liver
22	chr1:227205600-227220400	Weak transcription	Stomach Mucosa	stomach
23	chr1:227207600-227242000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr1:227208200-227216200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr1:227208600-227216200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr1:227208800-227216200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr1:227208800-227222600	Strong transcription	Cortex derived primary cultured neurospheres	brain
28	chr1:227209000-227216200	Weak transcription	HSMM	muscle
29	chr1:227209000-227231000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr1:227209000-227234600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr1:227209000-227272400	Weak transcription	Fetal Intestine Small	intestine
32	chr1:227209200-227216400	Weak transcription	Primary hematopoietic stem cells	blood
33	chr1:227209200-227301600	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr1:227209800-227222800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr1:227210200-227226400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr1:227210600-227245800	Weak transcription	NHEK	skin
37	chr1:227210800-227216400	Weak transcription	Fetal Kidney	kidney
38	chr1:227211000-227216200	Weak transcription	NHDF-Ad	bronchial
39	chr1:227212200-227223000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr1:227212600-227217000	Strong transcription	Fetal Muscle Leg	muscle
41	chr1:227212600-227217000	Strong transcription	Left Ventricle	heart
42	chr1:227212600-227217200	Strong transcription	Fetal Stomach	stomach
43	chr1:227212600-227217600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr1:227212800-227216000	Weak transcription	A549	lung
45	chr1:227212800-227226400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr1:227213000-227219200	Strong transcription	Liver	Liver
47	chr1:227213200-227222400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr1:227213400-227217400	Strong transcription	HUES64 Cell Line	embryonic stem cell
49	chr1:227213400-227220000	Strong transcription	HUES48 Cell Line	embryonic stem cell
50	chr1:227213600-227217000	Strong transcription	Osteobl	bone

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