Variant report

Variant	rs421521
Chromosome Location	chr5:94034827-94034828
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:94034610..94036248-chr5:94045168..94047165,2	K562	blood:

Variant related genes	Relation type
ENSG00000175471	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10037940	0.95[CEU][hapmap];0.88[CHB][hapmap];0.86[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10039102	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10039797	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10052066	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10062402	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10072894	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10078522	1.00[CEU][hapmap];0.92[CHB][hapmap];0.89[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1031389	0.91[CEU][hapmap]
rs10476614	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1124667	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11948061	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12189060	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1451734	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1549179	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2112448	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2112449	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2112450	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2636	0.88[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2638	0.88[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs306574	0.92[CEU][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs306578	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs395097	0.94[JPT][hapmap]
rs6556849	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs747880	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs755899	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs755901	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7709494	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7735924	0.83[CEU][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758002	chr5:93765205-94042201	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	esv2759354	chr5:93765205-94042201	Active TSS ZNF genes & repeats Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv462254	chr5:93956937-94056825	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv598953	chr5:93956937-94056825	ZNF genes & repeats Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv882387	chr5:94001476-94071404	Strong transcription Transcr. at gene 5' and 3' Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs421521	MCTP1	cis	normal skin	skin_eQTL
rs421521	MCTP1	cis	uninvolved skin	skin_eQTL
rs421521	MCTP1	cis	Temporal Cortex	GTEx
rs421521	MCTP1	Cis_1M	lymphoblastoid	RTeQTL
rs421521	MCTP1	cis	lesional skin	skin_eQTL
rs421521	MCTP1	cis	Cerebellum	GTEx
rs421521	ANKRD32	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:93991200-94049000	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr5:93994200-94047200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr5:93994400-94048800	Weak transcription	Small Intestine	intestine
4	chr5:93995600-94050400	Weak transcription	Esophagus	oesophagus
5	chr5:93996000-94036000	Weak transcription	GM12878-XiMat	blood
6	chr5:93996600-94048400	Weak transcription	Lung	lung
7	chr5:93996800-94036200	Weak transcription	Gastric	stomach
8	chr5:94008600-94038600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr5:94012600-94035000	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr5:94012600-94048400	Weak transcription	Aorta	Aorta
11	chr5:94012600-94048400	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr5:94012600-94049000	Weak transcription	Left Ventricle	heart
13	chr5:94012600-94051000	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr5:94012600-94053600	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr5:94020200-94048400	Weak transcription	Psoas Muscle	Psoas
16	chr5:94020800-94050000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr5:94023200-94045600	Weak transcription	Primary B cells from cord blood	blood
18	chr5:94023200-94046400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr5:94023200-94049800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr5:94023200-94050400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr5:94023200-94051000	Weak transcription	Thymus	Thymus
22	chr5:94023400-94035600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr5:94023400-94044200	Weak transcription	Primary T cells from cord blood	blood
24	chr5:94023400-94045000	Weak transcription	Fetal Muscle Trunk	muscle
25	chr5:94023400-94050400	Weak transcription	Fetal Muscle Leg	muscle
26	chr5:94023400-94051800	Weak transcription	Fetal Intestine Small	intestine
27	chr5:94024600-94046600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr5:94024600-94051800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr5:94025800-94036200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr5:94025800-94037800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr5:94025800-94046200	Weak transcription	Adipose Nuclei	Adipose
32	chr5:94025800-94050800	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr5:94025800-94050800	Weak transcription	K562	blood
34	chr5:94025800-94051400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr5:94026000-94038400	Weak transcription	Primary hematopoietic stem cells	blood
36	chr5:94026400-94051600	Weak transcription	Primary T helper cells PMA-I stimulated	--
37	chr5:94028000-94038600	Weak transcription	Fetal Lung	lung
38	chr5:94028000-94043000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr5:94028000-94050600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr5:94028000-94051600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr5:94028200-94037200	Weak transcription	Primary neutrophils fromperipheralblood	blood
42	chr5:94028800-94040200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr5:94029000-94051400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr5:94029200-94045800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr5:94029200-94049000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr5:94029200-94050400	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr5:94029200-94051800	Weak transcription	Brain Germinal Matrix	brain
48	chr5:94029200-94052400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr5:94029400-94035800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr5:94029400-94040400	Weak transcription	A549	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links