Variant report

Variant	rs10044797
Chromosome Location	chr5:94050702-94050703
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:94039956-94052296	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr5:94048115-94052802	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr5:94050692-94051142	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr5:94050520-94052703	K562	blood:	n/a	n/a
5	POLR2A	chr5:94039895-94052973	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:93951256..93953174-chr5:94050678..94052441,2	K562	blood:

Variant related genes	Relation type
MCTP1	TF binding region

Extended variants
information (count: 52 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10035632	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10037228	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10041262	0.87[ASN][1000 genomes]
rs10041551	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10041843	0.87[ASN][1000 genomes]
rs10051931	0.95[CEU][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10053484	0.91[CEU][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs10056685	0.90[CEU][hapmap]
rs10058130	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10058618	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10061737	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10062248	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10070258	0.91[CEU][hapmap];0.80[EUR][1000 genomes]
rs10076188	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10076461	0.87[ASN][1000 genomes]
rs10078049	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10078304	0.95[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10476612	0.90[CEU][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs10476613	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10476615	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11949227	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11955373	0.95[CEU][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11960129	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12516225	0.86[CEU][hapmap];0.80[EUR][1000 genomes]
rs12517866	0.91[CEU][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12518034	0.90[CEU][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12522312	0.91[CEU][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs13169956	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13353994	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13354061	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13358642	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13361811	0.95[CEU][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13362556	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28645132	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28787271	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs306573	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs306575	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4869218	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55974730	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6862592	0.87[ASN][1000 genomes]
rs6873364	0.90[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6879307	0.80[EUR][1000 genomes]
rs755898	0.95[CEU][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7705424	0.95[CEU][hapmap];0.80[EUR][1000 genomes]
rs7725095	0.95[CEU][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7725698	0.93[CEU][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7731360	0.90[EUR][1000 genomes]
rs7737779	0.91[CEU][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs9314118	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10044797	ANKRD32	Cis_1M	lymphoblastoid	RTeQTL
rs10044797	MCTP1	Cis_1M	lymphoblastoid	RTeQTL
rs10044797	ANKRD32	cis	multi-tissue	Pritchard

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:94012600-94051000	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr5:94012600-94053600	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr5:94023200-94051000	Weak transcription	Thymus	Thymus
4	chr5:94023400-94051800	Weak transcription	Fetal Intestine Small	intestine
5	chr5:94024600-94051800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr5:94025800-94050800	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr5:94025800-94050800	Weak transcription	K562	blood
8	chr5:94025800-94051400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr5:94026400-94051600	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr5:94028000-94051600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr5:94029000-94051400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr5:94029200-94051800	Weak transcription	Brain Germinal Matrix	brain
13	chr5:94029200-94052400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr5:94029400-94051200	Weak transcription	Fetal Brain Male	brain
15	chr5:94029400-94051400	Weak transcription	Fetal Heart	heart
16	chr5:94030200-94051400	Weak transcription	HSMM	muscle
17	chr5:94031000-94051200	Weak transcription	Duodenum Mucosa	Duodenum
18	chr5:94031000-94052000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr5:94034200-94051400	Weak transcription	Pancreas	Pancrea
20	chr5:94035400-94052000	Weak transcription	Fetal Kidney	kidney
21	chr5:94037400-94051000	Strong transcription	Primary monocytes fromperipheralblood	blood
22	chr5:94039000-94050800	Weak transcription	Stomach Smooth Muscle	stomach
23	chr5:94039000-94064600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr5:94039800-94052000	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr5:94040800-94052400	Weak transcription	Fetal Stomach	stomach
26	chr5:94041400-94051400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr5:94041800-94051600	Weak transcription	Brain Anterior Caudate	brain
28	chr5:94043200-94051000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr5:94043600-94051000	Strong transcription	Fetal Thymus	thymus
30	chr5:94043600-94053000	Weak transcription	GM12878-XiMat	blood
31	chr5:94043800-94059400	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr5:94044200-94051600	Weak transcription	HSMMtube	muscle
33	chr5:94044400-94052400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr5:94045600-94050800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr5:94045600-94052000	Weak transcription	Right Ventricle	heart
36	chr5:94046800-94052200	Weak transcription	Spleen	Spleen
37	chr5:94047000-94051200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr5:94047200-94050800	Weak transcription	Adipose Nuclei	Adipose
39	chr5:94047200-94055200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr5:94047600-94051200	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr5:94048400-94051000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr5:94048600-94071600	Weak transcription	Lung	lung
43	chr5:94048600-94081400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr5:94049000-94051000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr5:94049200-94050800	Weak transcription	Primary B cells from peripheral blood	blood
46	chr5:94049200-94050800	Weak transcription	Primary T helper cells fromperipheralblood	blood
47	chr5:94049200-94052000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr5:94049400-94051000	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr5:94049400-94051000	Weak transcription	Dnd41	blood
50	chr5:94049400-94051800	Weak transcription	HUES64 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links