Variant report

Variant	rs3816375
Chromosome Location	chr2:187505486-187505487
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:187505143..187506142-chr6:139309276..139309813,2	MCF-7	breast:
2	chr2:187465200..187467213-chr2:187503920..187506563,2	K562	blood:
3	chr2:187367118..187369155-chr2:187504848..187507189,2	K562	blood:
4	chr2:187359733..187361944-chr2:187503878..187506679,3	K562	blood:
5	chr2:187463714..187466700-chr2:187504985..187506563,2	K562	blood:
6	chr2:187496182..187500936-chr2:187502647..187507205,5	K562	blood:

Variant related genes	Relation type
ENSG00000135597	Chromatin interaction
ENSG00000138448	Chromatin interaction
ENSG00000213953	Chromatin interaction
ENSG00000268846	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10165992	0.88[CHB][hapmap]
rs1072901	0.88[CHB][hapmap]
rs10931253	0.88[ASN][1000 genomes]
rs12475476	0.94[CHB][hapmap]
rs12618322	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs12620821	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap];0.88[ASN][1000 genomes]
rs13020260	0.88[CHB][hapmap]
rs13028008	0.81[ASN][1000 genomes]
rs1448427	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.95[ASN][1000 genomes]
rs17406229	0.88[ASN][1000 genomes]
rs17406346	0.88[CHB][hapmap]
rs2121975	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap];0.88[ASN][1000 genomes]
rs2121976	0.88[CHB][hapmap]
rs2290083	0.93[EUR][1000 genomes]
rs2595395	0.88[CHB][hapmap]
rs2682873	0.88[CHB][hapmap]
rs3213964	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap]
rs34840521	0.95[ASN][1000 genomes]
rs35348196	0.95[ASN][1000 genomes]
rs35540241	0.83[ASN][1000 genomes]
rs3768785	0.88[CHB][hapmap];0.83[ASN][1000 genomes]
rs41265951	0.92[EUR][1000 genomes]
rs4667108	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4667109	0.91[EUR][1000 genomes]
rs55781198	0.83[ASN][1000 genomes]
rs55961288	0.84[ASN][1000 genomes]
rs56222785	0.93[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs6705757	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[JPT][hapmap];0.84[ASN][1000 genomes]
rs718259	0.88[CHB][hapmap]
rs7585442	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs7585471	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.86[YRI][hapmap];0.87[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs930657	1.00[CHB][hapmap];0.96[CHD][hapmap]
rs9789704	0.81[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	esv2757844	chr2:187332780-187580547	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	esv2759107	chr2:187332780-187580547	Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv875552	chr2:187393729-187505486	Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3816375	STRA6	trans	cerebellum	SCAN

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:187456200-187508600	Weak transcription	Esophagus	oesophagus
2	chr2:187456200-187533000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr2:187456600-187514000	Weak transcription	Thymus	Thymus
4	chr2:187456600-187520000	Weak transcription	Primary T helper cells fromperipheralblood	blood
5	chr2:187456800-187534400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr2:187457200-187506000	Weak transcription	Liver	Liver
7	chr2:187457200-187533800	Weak transcription	Spleen	Spleen
8	chr2:187458000-187511400	Weak transcription	Primary T helper cells PMA-I stimulated	--
9	chr2:187458000-187529000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr2:187459400-187505600	Weak transcription	NHLF	lung
11	chr2:187460200-187506200	Weak transcription	Small Intestine	intestine
12	chr2:187462800-187515400	Weak transcription	Gastric	stomach
13	chr2:187464800-187536200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr2:187465800-187529200	Weak transcription	Dnd41	blood
15	chr2:187466800-187533200	Weak transcription	Colonic Mucosa	Colon
16	chr2:187467200-187528600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr2:187467400-187515800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr2:187467600-187506000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr2:187471600-187521000	Weak transcription	Aorta	Aorta
20	chr2:187476000-187519800	Weak transcription	K562	blood
21	chr2:187476600-187508600	Weak transcription	Lung	lung
22	chr2:187476800-187536200	Weak transcription	Fetal Brain Male	brain
23	chr2:187482200-187533800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr2:187482800-187506000	Weak transcription	Fetal Kidney	kidney
25	chr2:187482800-187519600	Weak transcription	Brain Anterior Caudate	brain
26	chr2:187482800-187527800	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr2:187482800-187533200	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr2:187482800-187533600	Weak transcription	Rectal Smooth Muscle	rectum
29	chr2:187482800-187533800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr2:187482800-187533800	Weak transcription	Psoas Muscle	Psoas
31	chr2:187483400-187519800	Weak transcription	Brain Hippocampus Middle	brain
32	chr2:187486400-187506000	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr2:187486600-187531400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr2:187487200-187506200	Weak transcription	Primary neutrophils fromperipheralblood	blood
35	chr2:187487800-187510800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr2:187489400-187506000	Weak transcription	Primary T cells from cord blood	blood
37	chr2:187489400-187534400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr2:187490200-187506000	Weak transcription	Fetal Stomach	stomach
39	chr2:187490400-187508800	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr2:187491600-187506000	Weak transcription	Primary hematopoietic stem cells	blood
41	chr2:187493800-187529200	Weak transcription	Brain Substantia Nigra	brain
42	chr2:187494200-187529200	Weak transcription	Brain Germinal Matrix	brain
43	chr2:187494200-187535800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr2:187494800-187531800	Weak transcription	Brain Cingulate Gyrus	brain
45	chr2:187495000-187534400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr2:187499000-187506200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr2:187500000-187509800	Strong transcription	HUES64 Cell Line	embryonic stem cell
48	chr2:187500000-187510000	Strong transcription	NH-A	brain
49	chr2:187500000-187510200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr2:187500000-187513000	Strong transcription	HUVEC	blood vessel

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