Variant report

Variant	rs17022945
Chromosome Location	chr2:38806649-38806650
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:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:38806174..38811270-chr2:38966687..38973672,10	K562	blood:
2	chr2:38805174..38810149-chr2:38974397..38979817,14	K562	blood:
3	chr2:38802059..38810352-chr2:38974835..38979723,14	K562	blood:
4	chr2:38806398..38808518-chr2:38977015..38979696,2	MCF-7	breast:
5	chr2:38806069..38807840-chr2:38828104..38829708,2	MCF-7	breast:
6	chr2:38749021..38751091-chr2:38805998..38807763,2	K562	blood:
7	chr2:38600866..38603668-chr2:38806016..38808149,2	K562	blood:
8	chr2:38806614..38812442-chr2:38966843..38970976,5	K562	blood:
9	chr2:38788831..38791185-chr2:38805225..38808104,2	K562	blood:
10	chr2:38805084..38807176-chr2:38944983..38947545,2	K562	blood:
11	chr2:38805850..38810073-chr2:38814750..38818900,5	MCF-7	breast:
12	chr2:38806248..38808565-chr2:38954475..38956582,2	K562	blood:
13	chr2:38805216..38808046-chr2:38947623..38949999,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000143889	Chromatin interaction
ENSG00000119787	Chromatin interaction
ENSG00000235586	Chromatin interaction
ENSG00000115875	Chromatin interaction
ENSG00000152147	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1543880	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17576044	0.81[YRI][hapmap]
rs17603782	1.00[MEX][hapmap]
rs41446253	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55773228	0.92[AFR][1000 genomes]
rs55785223	0.87[AMR][1000 genomes]
rs55820712	0.84[AFR][1000 genomes]
rs55833813	0.87[AMR][1000 genomes]
rs55957936	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56251362	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56956410	0.87[AMR][1000 genomes]
rs59114683	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60475078	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6710613	0.81[YRI][hapmap]
rs6727765	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6730806	0.87[YRI][hapmap]
rs6732384	0.85[AMR][1000 genomes]
rs6732743	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72895897	0.87[AMR][1000 genomes]
rs72897608	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72897610	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72905837	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72905839	0.87[AMR][1000 genomes]
rs72905843	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72905844	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72905847	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72905860	0.88[AFR][1000 genomes]
rs72905861	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72905863	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72905868	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72905869	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72905871	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72905880	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72907906	0.81[AFR][1000 genomes]
rs73929040	0.87[AMR][1000 genomes]
rs73929050	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73929059	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs73929077	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73931606	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs7578356	1.00[MEX][hapmap]
rs7579589	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs7584862	1.00[MEX][hapmap]
rs7586241	0.93[YRI][hapmap]
rs7594264	0.88[AFR][1000 genomes];0.85[AMR][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	nsv916059	chr2:38332341-39119398	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	143 gene(s)	inside rSNPs	diseases
2	nsv9646	chr2:38358311-39082189	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Strong transcription 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 miRNA target site	141 gene(s)	inside rSNPs	diseases
3	nsv873881	chr2:38745624-38877636	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
4	nsv581482	chr2:38799820-38858669	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv581483	chr2:38799820-38862223	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv581484	chr2:38799820-38874177	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17022945	RNF212	trans	lymphoblastoid	seeQTL

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:38763600-38809600	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr2:38768200-38812800	Weak transcription	Psoas Muscle	Psoas
3	chr2:38775800-38821800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr2:38777000-38807200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr2:38779000-38818200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr2:38779400-38821800	Weak transcription	Right Ventricle	heart
7	chr2:38779600-38807400	Weak transcription	Fetal Heart	heart
8	chr2:38779600-38812800	Weak transcription	Aorta	Aorta
9	chr2:38781200-38827600	Weak transcription	Esophagus	oesophagus
10	chr2:38782400-38819000	Strong transcription	Fetal Thymus	thymus
11	chr2:38783800-38827800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr2:38785000-38827600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr2:38786000-38827600	Weak transcription	Colonic Mucosa	Colon
14	chr2:38786400-38818800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr2:38786600-38819000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr2:38787200-38807000	Strong transcription	HUES48 Cell Line	embryonic stem cell
17	chr2:38787200-38807000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
18	chr2:38790800-38807000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
19	chr2:38792600-38810200	Strong transcription	K562	blood
20	chr2:38795200-38807200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr2:38795200-38808400	Weak transcription	Left Ventricle	heart
22	chr2:38795200-38808400	Weak transcription	Lung	lung
23	chr2:38795200-38808400	Weak transcription	Ovary	ovary
24	chr2:38795200-38809200	Weak transcription	Fetal Intestine Small	intestine
25	chr2:38795200-38809200	Weak transcription	Fetal Stomach	stomach
26	chr2:38795200-38814800	Weak transcription	Gastric	stomach
27	chr2:38795400-38808200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr2:38795600-38808400	Weak transcription	Brain Cingulate Gyrus	brain
29	chr2:38796200-38808200	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr2:38796400-38808400	Weak transcription	Brain Angular Gyrus	brain
31	chr2:38796400-38812800	Weak transcription	Small Intestine	intestine
32	chr2:38796600-38808600	Weak transcription	Brain Hippocampus Middle	brain
33	chr2:38798000-38808000	Weak transcription	Colon Smooth Muscle	Colon
34	chr2:38798000-38818000	Weak transcription	Stomach Mucosa	stomach
35	chr2:38798000-38827600	Weak transcription	Spleen	Spleen
36	chr2:38798200-38808000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr2:38798200-38808400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr2:38798200-38808400	Weak transcription	Pancreas	Pancrea
39	chr2:38798200-38812800	Weak transcription	Fetal Muscle Leg	muscle
40	chr2:38798200-38812800	Weak transcription	Thymus	Thymus
41	chr2:38798200-38820600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr2:38798200-38821800	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr2:38798200-38827600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr2:38798600-38808000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr2:38798600-38808000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr2:38798600-38808200	Weak transcription	Stomach Smooth Muscle	stomach
47	chr2:38798600-38816400	Weak transcription	Brain Germinal Matrix	brain
48	chr2:38798800-38808200	Weak transcription	Fetal Brain Female	brain
49	chr2:38798800-38817000	Weak transcription	Brain Anterior Caudate	brain
50	chr2:38798800-38822000	Weak transcription	NHEK	skin

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