Variant report

Variant	rs6844261
Chromosome Location	chr4:99498680-99498681
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:99496585..99499120-chr4:99503712..99505800,2	MCF-7	breast:

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10004753	0.89[JPT][hapmap]
rs10005781	0.89[JPT][hapmap]
rs10026446	1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs11943162	0.81[CEU][hapmap]
rs13116201	0.89[JPT][hapmap]
rs1358548	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17192060	0.81[JPT][hapmap]
rs4699353	0.82[MEX][hapmap]
rs6532751	0.81[CEU][hapmap];0.83[MEX][hapmap]
rs7668981	0.81[JPT][hapmap]
rs7669964	0.85[CEU][hapmap]
rs7695093	0.81[JPT][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	esv2754250	chr4:99094922-99527122	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv1004181	chr4:99208152-99529576	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	esv2760882	chr4:99460485-99521345	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6844261	TSPAN5	cis	cerebellum	SCAN

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:99466800-99501600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr4:99479000-99506400	Weak transcription	Aorta	Aorta
3	chr4:99483400-99498800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr4:99485000-99501400	Weak transcription	HUVEC	blood vessel
5	chr4:99487200-99500000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr4:99488000-99499000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr4:99488000-99499200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr4:99488200-99500200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr4:99489000-99498800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr4:99490200-99499000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr4:99490400-99499200	Weak transcription	Brain Germinal Matrix	brain
12	chr4:99490600-99498800	Weak transcription	Stomach Mucosa	stomach
13	chr4:99490600-99501400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr4:99490800-99499600	Weak transcription	Fetal Muscle Trunk	muscle
15	chr4:99490800-99499800	Weak transcription	Right Atrium	heart
16	chr4:99490800-99506600	Weak transcription	Esophagus	oesophagus
17	chr4:99490800-99509000	Weak transcription	HSMM	muscle
18	chr4:99491000-99503400	Weak transcription	Thymus	Thymus
19	chr4:99492000-99499200	Weak transcription	Osteobl	bone
20	chr4:99492400-99498800	Weak transcription	Primary T helper cells PMA-I stimulated	--
21	chr4:99492600-99499800	Weak transcription	Spleen	Spleen
22	chr4:99492600-99500200	Weak transcription	Fetal Brain Female	brain
23	chr4:99492600-99501800	Weak transcription	Primary B cells from cord blood	blood
24	chr4:99493200-99501400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr4:99493600-99498800	Weak transcription	Brain Hippocampus Middle	brain
26	chr4:99493600-99500400	Weak transcription	Primary hematopoietic stem cells	blood
27	chr4:99493600-99501400	Weak transcription	Fetal Thymus	thymus
28	chr4:99493800-99498800	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr4:99494000-99499200	Weak transcription	Fetal Lung	lung
30	chr4:99495200-99500200	Weak transcription	HMEC	breast
31	chr4:99495800-99499000	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr4:99495800-99499800	Weak transcription	NHEK	skin
33	chr4:99496000-99498800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr4:99496000-99499000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr4:99496000-99502000	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr4:99496000-99502000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr4:99496200-99498800	Weak transcription	Fetal Stomach	stomach
38	chr4:99496200-99499000	Weak transcription	Primary T helper cells fromperipheralblood	blood
39	chr4:99496200-99499200	Weak transcription	NH-A	brain
40	chr4:99496200-99499800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr4:99496200-99500000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr4:99496200-99500400	Weak transcription	Fetal Brain Male	brain
43	chr4:99496200-99501400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr4:99496200-99501400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr4:99496200-99502200	Weak transcription	Primary T cells from cord blood	blood
46	chr4:99496400-99498800	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr4:99496400-99503000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr4:99496600-99498800	Weak transcription	NHDF-Ad	bronchial
49	chr4:99496600-99499800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr4:99496800-99504600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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