Variant report

Variant	rs6582622
Chromosome Location	chr12:46605239-46605240
allele	C/T
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:46604571..46607564-chr12:46643958..46646763,2	MCF-7	breast:
2	chr12:46595584..46597824-chr12:46604968..46606668,2	K562	blood:
3	chr12:46603045..46606011-chr12:46660345..46662347,2	K562	blood:
4	chr12:46598504..46606384-chr12:46660159..46664661,13	MCF-7	breast:
5	chr12:46601918..46605358-chr12:46605865..46610216,5	MCF-7	breast:
6	chr12:46593902..46597897-chr12:46605177..46609280,4	MCF-7	breast:
7	chr12:46601000..46609556-chr12:46658880..46665180,16	MCF-7	breast:
8	chr12:46604867..46608116-chr12:46608247..46612042,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000111371	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs4768106	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4768107	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6582623	0.84[CEU][hapmap]
rs7971399	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7979418	0.82[YRI][hapmap]
rs960117	1.00[CHB][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];0.82[JPT][hapmap];0.89[MEX][hapmap];0.83[TSI][hapmap];0.97[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs962683	0.82[ASW][hapmap];1.00[CHB][hapmap];0.89[GIH][hapmap];0.88[LWK][hapmap];0.89[MEX][hapmap];0.92[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs963326	1.00[CHB][hapmap];0.82[GIH][hapmap];0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2754441	chr12:46590364-46605239	Strong transcription ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6582622	IRAK4	cis	cerebellum	SCAN

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:46589800-46608400	Weak transcription	Primary monocytes fromperipheralblood	blood
2	chr12:46590800-46613200	Strong transcription	Hela-S3	cervix
3	chr12:46591000-46613200	Strong transcription	HUES6 Cell Line	embryonic stem cell
4	chr12:46591000-46613600	Weak transcription	Fetal Brain Male	brain
5	chr12:46591000-46613600	Weak transcription	Gastric	stomach
6	chr12:46592400-46609800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr12:46592400-46613400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr12:46592600-46606200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr12:46592800-46654200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr12:46596000-46618200	Weak transcription	Aorta	Aorta
11	chr12:46597400-46614200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr12:46597600-46659600	Weak transcription	Colonic Mucosa	Colon
13	chr12:46598800-46606400	Weak transcription	Primary neutrophils fromperipheralblood	blood
14	chr12:46599400-46606400	Enhancers	Fetal Heart	heart
15	chr12:46600000-46613600	Weak transcription	NHLF	lung
16	chr12:46600600-46607400	Weak transcription	Fetal Kidney	kidney
17	chr12:46601200-46606600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr12:46601200-46613200	Weak transcription	NH-A	brain
19	chr12:46601400-46606000	Weak transcription	Fetal Intestine Large	intestine
20	chr12:46601400-46613200	Weak transcription	Fetal Brain Female	brain
21	chr12:46601600-46606200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr12:46601600-46606200	Weak transcription	Primary hematopoietic stem cells	blood
23	chr12:46601600-46607000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
24	chr12:46601600-46607800	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
25	chr12:46601800-46605400	Enhancers	Colon Smooth Muscle	Colon
26	chr12:46602600-46606000	Enhancers	Primary T helper cells fromperipheralblood	blood
27	chr12:46602800-46605400	Enhancers	Rectal Smooth Muscle	rectum
28	chr12:46603000-46605400	Genic enhancers	NHEK	skin
29	chr12:46603000-46607400	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
30	chr12:46603200-46605600	Enhancers	Fetal Intestine Small	intestine
31	chr12:46603200-46605600	Enhancers	Fetal Muscle Leg	muscle
32	chr12:46603200-46605600	Enhancers	Skeletal Muscle Male	skeletal muscle
33	chr12:46603200-46606200	Enhancers	Small Intestine	intestine
34	chr12:46603400-46606200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr12:46603600-46605400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr12:46603600-46605800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr12:46603600-46612200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr12:46603800-46605600	Enhancers	Duodenum Mucosa	Duodenum
39	chr12:46603800-46605600	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
40	chr12:46604000-46606800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr12:46604000-46607400	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
42	chr12:46604000-46608600	Weak transcription	Right Ventricle	heart
43	chr12:46604000-46608800	Weak transcription	Right Atrium	heart
44	chr12:46604000-46609800	Weak transcription	Psoas Muscle	Psoas
45	chr12:46604000-46610000	Weak transcription	Lung	lung
46	chr12:46604000-46610200	Weak transcription	Brain Germinal Matrix	brain
47	chr12:46604000-46613400	Weak transcription	Brain Angular Gyrus	brain
48	chr12:46604000-46623400	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr12:46604000-46633800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr12:46604000-46637400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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