Variant report

Variant	rs3224
Chromosome Location	chr6:45869630-45869631
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:45533886..45534863-chr6:45869333..45869893,2	Hela-S3	cervix:

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs12665031	0.84[CEU][hapmap]
rs1416167	0.84[CEU][hapmap]
rs3729618	0.84[CEU][hapmap]
rs3777544	0.96[CEU][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3777561	0.84[CEU][hapmap]
rs3822876	0.84[CEU][hapmap]
rs3822878	0.84[CEU][hapmap]
rs3822880	0.81[CEU][hapmap]
rs3957316	0.86[EUR][1000 genomes]
rs4269369	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4371841	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4473854	0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56178742	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56253836	0.92[EUR][1000 genomes]
rs6458474	0.92[EUR][1000 genomes]
rs6909217	0.83[ASN][1000 genomes]
rs9367228	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9369588	0.92[EUR][1000 genomes]
rs9463147	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv532024	chr6:45475088-45982640	Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3224	GALE	cis	Temporal Cortex	GTEx

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:45865000-45870000	Weak transcription	Duodenum Mucosa	Duodenum
2	chr6:45865200-45870000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr6:45865200-45870000	Weak transcription	HSMMtube	muscle
4	chr6:45865400-45870000	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr6:45866200-45871000	Enhancers	HUES6 Cell Line	embryonic stem cell
6	chr6:45866400-45880000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr6:45866600-45870000	Enhancers	HUES64 Cell Line	embryonic stem cell
8	chr6:45866600-45898400	Weak transcription	Colonic Mucosa	Colon
9	chr6:45867000-45869800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
10	chr6:45867000-45869800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr6:45867000-45871200	Strong transcription	Fetal Intestine Small	intestine
12	chr6:45867200-45870200	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
13	chr6:45867400-45870000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr6:45867400-45870400	Genic enhancers	Left Ventricle	heart
15	chr6:45867600-45869800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr6:45867600-45870200	Weak transcription	Placenta	Placenta
17	chr6:45867800-45870000	Weak transcription	Brain Germinal Matrix	brain
18	chr6:45867800-45870600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr6:45867800-45871000	Strong transcription	Fetal Intestine Large	intestine
20	chr6:45867800-45884200	Weak transcription	Fetal Heart	heart
21	chr6:45868200-45870000	Enhancers	H1 Cell Line	embryonic stem cell
22	chr6:45868200-45870000	Weak transcription	Lung	lung
23	chr6:45868600-45869800	Enhancers	H9 Cell Line	embryonic stem cell
24	chr6:45868600-45870000	Enhancers	iPS-15b Cell Line	embryonic stem cell
25	chr6:45868600-45870400	Enhancers	Breast Myoepithelial Primary Cells	Breast
26	chr6:45868600-45870800	Enhancers	Fetal Muscle Leg	muscle
27	chr6:45868600-45871200	Enhancers	Psoas Muscle	Psoas
28	chr6:45868800-45870000	Enhancers	HSMM	muscle
29	chr6:45868800-45889600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr6:45869000-45870400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr6:45869000-45870400	Genic enhancers	Right Ventricle	heart
32	chr6:45869000-45871000	Enhancers	Skeletal Muscle Female	skeletal muscle
33	chr6:45869000-45879600	Weak transcription	Adipose Nuclei	Adipose
34	chr6:45869200-45870200	Enhancers	Fetal Muscle Trunk	muscle
35	chr6:45869200-45871400	Strong transcription	Rectal Mucosa Donor 29	rectum
36	chr6:45869200-45871400	Genic enhancers	Skeletal Muscle Male	skeletal muscle
37	chr6:45869400-45869800	Enhancers	iPS-20b Cell Line	embryonic stem cell
38	chr6:45869400-45870000	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
39	chr6:45869400-45870200	Weak transcription	Right Atrium	heart
40	chr6:45869600-45869800	Enhancers	ES-I3 Cell Line	embryonic stem cell
41	chr6:45869600-45870200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr6:45869600-45871000	Strong transcription	Sigmoid Colon	Sigmoid Colon

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