Variant report

Variant	rs2531757
Chromosome Location	chr3:45850520-45850521
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:45817620..45820058-chr3:45848414..45850777,2	K562	blood:
2	chr3:45841159..45843943-chr3:45848484..45850929,2	MCF-7	breast:

Extended variants
information (count: 5 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs2014591	0.95[ASN][1000 genomes]
rs2531741	0.80[ASN][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	nsv876734	chr3:45725031-46468467	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv498008	chr3:45733423-46319401	Strong transcription Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv834678	chr3:45804294-46010256	Enhancers Flanking Bivalent TSS/Enh Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2531757	CCR1	cis	cerebellum	SCAN
rs2531757	CDC25A	cis	cerebellum	SCAN
rs2531757	CXCR6	cis	parietal	SCAN
rs2531757	C3orf39	cis	cerebellum	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:45838400-45860000	Weak transcription	Gastric	stomach
2	chr3:45842400-45857400	Weak transcription	Duodenum Mucosa	Duodenum
3	chr3:45842400-45859200	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr3:45842400-45859800	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr3:45842600-45854400	Weak transcription	Fetal Intestine Large	intestine
6	chr3:45843800-45856400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr3:45844000-45857400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr3:45845400-45853600	Weak transcription	Fetal Intestine Small	intestine
9	chr3:45845400-45858800	Weak transcription	Brain Germinal Matrix	brain
10	chr3:45846600-45857400	Weak transcription	Fetal Brain Female	brain
11	chr3:45847800-45871400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr3:45848000-45864400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr3:45848200-45850600	Enhancers	Thymus	Thymus
14	chr3:45848600-45860800	Weak transcription	Primary T cells from cord blood	blood
15	chr3:45849400-45857400	Weak transcription	Fetal Stomach	stomach
16	chr3:45849400-45857600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr3:45849400-45859000	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr3:45849400-45864800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr3:45849400-45875200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr3:45849600-45857400	Weak transcription	HSMMtube	muscle
21	chr3:45849600-45857800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr3:45849600-45862400	Weak transcription	Fetal Lung	lung
23	chr3:45849800-45857400	Weak transcription	Stomach Smooth Muscle	stomach
24	chr3:45849800-45871800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr3:45850000-45851400	Strong transcription	Dnd41	blood
26	chr3:45850000-45857400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr3:45850000-45857600	Weak transcription	Fetal Muscle Leg	muscle
28	chr3:45850000-45859000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr3:45850000-45859000	Weak transcription	Brain Substantia Nigra	brain
30	chr3:45850000-45859800	Weak transcription	Small Intestine	intestine
31	chr3:45850200-45852000	Weak transcription	Fetal Thymus	thymus
32	chr3:45850200-45857400	Weak transcription	Brain Anterior Caudate	brain
33	chr3:45850200-45857400	Weak transcription	Psoas Muscle	Psoas
34	chr3:45850200-45857600	Weak transcription	Brain Angular Gyrus	brain
35	chr3:45850200-45857600	Weak transcription	Brain Hippocampus Middle	brain
36	chr3:45850200-45862200	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr3:45850200-45866200	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr3:45850200-45867800	Weak transcription	Brain Cingulate Gyrus	brain
39	chr3:45850400-45857600	Weak transcription	Aorta	Aorta
40	chr3:45850400-45857600	Weak transcription	Pancreas	Pancrea

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links