Variant report

Variant	rs2531848
Chromosome Location	chr22:30032484-30032485
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:29998526..30000327-chr22:30030498..30033329,2	MCF-7	breast:
2	chr22:30021415..30023125-chr22:30030680..30033150,2	K562	blood:

Variant related genes	Relation type
ENSG00000186575	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1006396	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10427824	0.91[AFR][1000 genomes]
rs1049534	0.86[JPT][hapmap]
rs11704899	0.94[CEU][hapmap];0.90[TSI][hapmap]
rs11705569	0.87[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap]
rs16987752	1.00[YRI][hapmap]
rs16987832	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2072303	1.00[YRI][hapmap]
rs2074947	1.00[YRI][hapmap]
rs2074948	0.86[JPT][hapmap]
rs2074949	1.00[YRI][hapmap]
rs2074950	1.00[YRI][hapmap]
rs2247753	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2267146	1.00[YRI][hapmap]
rs2267152	0.88[CEU][hapmap];0.83[TSI][hapmap]
rs2270079	1.00[YRI][hapmap]
rs2302140	1.00[YRI][hapmap]
rs2302141	0.86[JPT][hapmap]
rs2302142	1.00[YRI][hapmap]
rs2527336	0.87[CEU][hapmap]
rs2530656	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2530658	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2530664	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2531849	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs456285	0.82[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.82[TSI][hapmap]
rs456585	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs458196	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs460428	0.83[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap]
rs462444	0.83[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap]
rs463220	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs468254	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs468692	0.87[CHB][hapmap];0.95[JPT][hapmap]
rs468795	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs468852	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs469363	0.86[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.81[MEX][hapmap];0.82[TSI][hapmap]
rs5763297	0.86[JPT][hapmap]
rs5763301	0.86[JPT][hapmap];0.82[TSI][hapmap]
rs5763303	0.86[JPT][hapmap]
rs5763305	0.94[CEU][hapmap];0.96[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs5763306	0.86[JPT][hapmap]
rs57995869	0.91[AFR][1000 genomes]
rs7609	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs8135828	0.94[CEU][hapmap];0.96[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][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	nsv529742	chr22:29677909-30274388	Bivalent Enhancer Enhancers ZNF genes & repeats Strong transcription Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1062373	chr22:29826745-30092448	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv544676	chr22:29826745-30092448	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers 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	20 gene(s)	inside rSNPs	diseases
4	nsv1064081	chr22:29826745-30623965	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
5	nsv544677	chr22:29826745-30623965	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
6	nsv834172	chr22:29899036-30057948	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv817417	chr22:29998464-30035142	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs2531848	THOC5	cis	lung	GTEx
rs2531848	NIPSNAP1	cis	cerebellum	SCAN
rs2531848	CABP7	cis	cerebellum	SCAN
rs2531848	THOC5	cis	Artery Aorta	GTEx
rs2531848	NIPSNAP1	cis	Stomach	GTEx
rs2531848	THOC5	cis	Adipose Subcutaneous	GTEx
rs2531848	THOC5	cis	Muscle Skeletal	GTEx
rs2531848	THOC5	cis	Artery Tibial	GTEx
rs2531848	THOC5	cis	Nerve Tibial	GTEx
rs2531848	THOC5	cis	Esophagus Muscularis	GTEx

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30003800-30032800	Weak transcription	Fetal Muscle Trunk	muscle
2	chr22:30014400-30085800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr22:30018000-30069200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr22:30018400-30033400	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr22:30019800-30033800	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr22:30020200-30033200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr22:30020200-30033600	Weak transcription	GM12878-XiMat	blood
8	chr22:30020200-30057000	Weak transcription	Psoas Muscle	Psoas
9	chr22:30020200-30064200	Weak transcription	Small Intestine	intestine
10	chr22:30020400-30032800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr22:30020400-30033400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr22:30020600-30032800	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr22:30020800-30097000	Weak transcription	Stomach Mucosa	stomach
14	chr22:30021200-30033200	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr22:30021800-30032800	Weak transcription	Liver	Liver
16	chr22:30021800-30041600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr22:30022000-30033400	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr22:30022000-30037200	Weak transcription	Primary neutrophils fromperipheralblood	blood
19	chr22:30022000-30038400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr22:30022200-30053400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr22:30022400-30032800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr22:30022800-30034000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr22:30023000-30037400	Weak transcription	Hela-S3	cervix
24	chr22:30023200-30038600	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr22:30023400-30032800	Weak transcription	Aorta	Aorta
26	chr22:30023600-30032800	Weak transcription	Ovary	ovary
27	chr22:30023600-30037800	Weak transcription	Brain Cingulate Gyrus	brain
28	chr22:30023800-30032800	Weak transcription	HSMMtube	muscle
29	chr22:30023800-30038200	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr22:30023800-30038600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr22:30024000-30034800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr22:30024000-30037400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr22:30024200-30032800	Weak transcription	Primary B cells from cord blood	blood
34	chr22:30024200-30038200	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr22:30024400-30033000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr22:30024600-30034600	Weak transcription	HMEC	breast
37	chr22:30025800-30033600	Weak transcription	Primary T helper cells PMA-I stimulated	--
38	chr22:30025800-30033800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr22:30026000-30033400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr22:30026200-30033800	Weak transcription	Fetal Lung	lung
41	chr22:30026400-30038000	Weak transcription	Brain Angular Gyrus	brain
42	chr22:30026800-30035200	Weak transcription	Fetal Stomach	stomach
43	chr22:30026800-30038200	Weak transcription	Spleen	Spleen
44	chr22:30026800-30055800	Weak transcription	Gastric	stomach
45	chr22:30027000-30032800	Weak transcription	Right Ventricle	heart
46	chr22:30027200-30044400	Weak transcription	Brain Substantia Nigra	brain
47	chr22:30027400-30032800	Weak transcription	Stomach Smooth Muscle	stomach
48	chr22:30027400-30033000	Weak transcription	Lung	lung
49	chr22:30027400-30038000	Weak transcription	Colon Smooth Muscle	Colon
50	chr22:30027600-30033400	Weak transcription	Brain Inferior Temporal Lobe	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links