Variant report

Variant	rs309273
Chromosome Location	chr2:7200864-7200865
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs2460409	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2460410	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28293	0.83[EUR][1000 genomes]
rs309263	0.82[EUR][1000 genomes]
rs309264	0.82[EUR][1000 genomes]
rs309268	0.84[EUR][1000 genomes]
rs309276	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs309283	0.83[EUR][1000 genomes]
rs309284	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs309293	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs309304	0.85[CEU][hapmap]
rs417248	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs432588	0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs434382	0.85[CEU][hapmap];0.80[MEX][hapmap]

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	nsv469394	chr2:7197199-7230988	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv580914	chr2:7197199-7230988	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv915888	chr2:7197783-7461967	Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs309273	RNF144A	cis	cerebellum	SCAN

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:7189400-7203200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr2:7189400-7213800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr2:7194200-7234000	Weak transcription	Pancreas	Pancrea
4	chr2:7194400-7202200	Weak transcription	Ovary	ovary
5	chr2:7194400-7210800	Weak transcription	Lung	lung
6	chr2:7194600-7201800	Weak transcription	Fetal Kidney	kidney
7	chr2:7194600-7206400	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr2:7194800-7202800	Weak transcription	Brain Hippocampus Middle	brain
9	chr2:7195000-7217000	Weak transcription	Fetal Muscle Leg	muscle
10	chr2:7195600-7201000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
11	chr2:7196800-7202000	Weak transcription	Right Atrium	heart
12	chr2:7198000-7202200	Weak transcription	Adipose Nuclei	Adipose
13	chr2:7198600-7201000	Enhancers	Primary T helper cells fromperipheralblood	blood
14	chr2:7199600-7201000	Enhancers	Aorta	Aorta
15	chr2:7199800-7202200	Weak transcription	Psoas Muscle	Psoas
16	chr2:7199800-7203400	Enhancers	Fetal Stomach	stomach
17	chr2:7200000-7203200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr2:7200000-7203400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr2:7200000-7203400	Weak transcription	Fetal Thymus	thymus
20	chr2:7200200-7201400	Enhancers	iPS-18 Cell Line	embryonic stem cell
21	chr2:7200200-7203200	Weak transcription	Primary hematopoietic stem cells	blood
22	chr2:7200400-7201000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr2:7200400-7202400	Strong transcription	Dnd41	blood
24	chr2:7200400-7203600	Enhancers	Colon Smooth Muscle	Colon
25	chr2:7200400-7203600	Enhancers	Rectal Smooth Muscle	rectum
26	chr2:7200600-7201200	Enhancers	HUES48 Cell Line	embryonic stem cell
27	chr2:7200600-7201200	Enhancers	HUES64 Cell Line	embryonic stem cell
28	chr2:7200600-7201200	Enhancers	iPS-20b Cell Line	embryonic stem cell
29	chr2:7200600-7201400	Enhancers	H1 Cell Line	embryonic stem cell
30	chr2:7200600-7202800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr2:7200600-7203200	Weak transcription	Primary T helper cells PMA-I stimulated	--
32	chr2:7200600-7204000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr2:7200800-7201000	Enhancers	Left Ventricle	heart
34	chr2:7200800-7201200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
35	chr2:7200800-7201200	Enhancers	Stomach Smooth Muscle	stomach
36	chr2:7200800-7201200	Enhancers	Thymus	Thymus
37	chr2:7200800-7202200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr2:7200800-7203200	Weak transcription	Primary T cells from cord blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links