Variant report

Variant	rs41404047
Chromosome Location	chr5:58855925-58855926
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	chr5:58853948..58856765-chr5:58857609..58860199,2	MCF-7	breast:

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1035321	0.83[CEU][hapmap];0.94[MEX][hapmap]
rs10491440	0.83[CEU][hapmap]
rs10491441	0.83[CEU][hapmap]
rs10491442	0.83[CEU][hapmap]
rs10514859	0.83[CEU][hapmap];0.94[MEX][hapmap]
rs11950308	0.83[CEU][hapmap]
rs11957151	0.83[CEU][hapmap]
rs12520633	0.83[CEU][hapmap];0.83[MEX][hapmap]
rs159393	0.98[ASN][1000 genomes]
rs172363	0.85[CHB][hapmap]
rs17741863	0.83[CEU][hapmap]
rs17797996	0.83[CEU][hapmap]
rs291117	0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs291118	0.88[CHB][hapmap]
rs291119	0.89[CHB][hapmap]
rs291120	0.89[CHB][hapmap]
rs294476	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs294503	1.00[CHB][hapmap];0.88[CHD][hapmap];0.98[ASN][1000 genomes]
rs295949	0.88[CHB][hapmap]
rs295977	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap]
rs36081664	0.83[CEU][hapmap];0.94[MEX][hapmap]
rs893190	0.83[CEU][hapmap];0.83[MEX][hapmap]

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	nsv598254	chr5:58715782-58923601	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv881706	chr5:58730111-58865857	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv1031631	chr5:58783629-59015470	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA	4 gene(s)	inside rSNPs	diseases
4	nsv462189	chr5:58830145-58879822	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv598255	chr5:58830145-58879822	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs41404047	IGDCC4	trans	cerebellum	SCAN

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58836800-58857400	Weak transcription	Primary B cells from cord blood	blood
2	chr5:58840200-58858800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr5:58840400-58856200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr5:58840800-58858600	Weak transcription	Fetal Kidney	kidney
5	chr5:58843800-58862400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr5:58845200-58856200	Weak transcription	Hela-S3	cervix
7	chr5:58845600-58858200	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr5:58850200-58858200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr5:58850400-58856400	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr5:58850400-58860800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr5:58850600-58856200	Weak transcription	Fetal Intestine Large	intestine
12	chr5:58850800-58856200	Weak transcription	Fetal Intestine Small	intestine
13	chr5:58851600-58858600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr5:58851800-58856200	Weak transcription	Brain Angular Gyrus	brain
15	chr5:58851800-58856200	Weak transcription	Brain Hippocampus Middle	brain
16	chr5:58851800-58857800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr5:58851800-58858600	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr5:58851800-58859800	Weak transcription	Psoas Muscle	Psoas
19	chr5:58853400-58858400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr5:58853400-58858400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr5:58853800-58858200	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr5:58853800-58858400	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr5:58853800-58858600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr5:58854000-58858800	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr5:58854400-58856800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr5:58854400-58857200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr5:58854400-58858000	Enhancers	HUVEC	blood vessel
28	chr5:58854600-58856000	Enhancers	Fetal Lung	lung
29	chr5:58854600-58856200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
30	chr5:58854600-58861600	Weak transcription	Fetal Brain Female	brain
31	chr5:58854800-58856800	Enhancers	Stomach Mucosa	stomach
32	chr5:58854800-58857000	Transcr. at gene 5' and 3'	A549	lung
33	chr5:58854800-58857200	Weak transcription	Fetal Brain Male	brain
34	chr5:58854800-58857400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr5:58854800-58858600	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr5:58855000-58858400	Weak transcription	HMEC	breast
37	chr5:58855200-58856600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr5:58855200-58857000	Enhancers	ES-I3 Cell Line	embryonic stem cell
39	chr5:58855400-58856000	Enhancers	Adipose Nuclei	Adipose
40	chr5:58855400-58856200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr5:58855400-58856600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr5:58855400-58857200	Enhancers	HepG2	liver
43	chr5:58855600-58856000	Enhancers	HUES64 Cell Line	embryonic stem cell
44	chr5:58855600-58856000	Enhancers	Brain Anterior Caudate	brain
45	chr5:58855600-58856600	Enhancers	Brain Cingulate Gyrus	brain
46	chr5:58855600-58863000	Enhancers	Primary B cells from peripheral blood	blood
47	chr5:58855800-58856000	Enhancers	Small Intestine	intestine
48	chr5:58855800-58856600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr5:58855800-58856600	Enhancers	Gastric	stomach
50	chr5:58855800-58857000	Enhancers	Brain Substantia Nigra	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links