Variant report

Variant	rs3861401
Chromosome Location	chr6:143015405-143015406
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 4 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs2202900	1.00[JPT][hapmap]
rs3900871	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949088	chr6:142561402-143128849	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv830828	chr6:142970134-143116517	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3861401	SF3B5	cis	parietal	SCAN

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:143012800-143016000	Enhancers	Primary T cells from cord blood	blood
2	chr6:143013800-143015800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr6:143014200-143015600	Enhancers	HUVEC	blood vessel
4	chr6:143014200-143015800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
5	chr6:143014200-143015800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr6:143014200-143015800	Flanking Active TSS	NH-A	brain
7	chr6:143014200-143016000	Enhancers	Primary T helper cells PMA-I stimulated	--
8	chr6:143014200-143016600	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr6:143014200-143017200	Enhancers	Fetal Brain Male	brain
10	chr6:143014200-143017600	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr6:143014200-143018000	Enhancers	HSMM	muscle
12	chr6:143014200-143019800	Enhancers	Fetal Stomach	stomach
13	chr6:143014400-143015600	Weak transcription	Ovary	ovary
14	chr6:143014400-143016000	Enhancers	GM12878-XiMat	blood
15	chr6:143014400-143016600	Enhancers	HMEC	breast
16	chr6:143014400-143017400	Weak transcription	Brain Anterior Caudate	brain
17	chr6:143014400-143017600	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr6:143014400-143018200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr6:143014400-143018800	Weak transcription	Brain Cingulate Gyrus	brain
20	chr6:143014400-143023800	Weak transcription	Right Atrium	heart
21	chr6:143014400-143028200	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr6:143014600-143015600	Weak transcription	Primary T cells fromperipheralblood	blood
23	chr6:143014600-143015600	Weak transcription	Rectal Smooth Muscle	rectum
24	chr6:143014600-143015600	Weak transcription	Monocytes-CD14+_RO01746	blood
25	chr6:143014600-143015800	Weak transcription	Stomach Smooth Muscle	stomach
26	chr6:143014600-143016000	Weak transcription	Brain Hippocampus Middle	brain
27	chr6:143014600-143016400	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr6:143014600-143016600	Weak transcription	Fetal Kidney	kidney
29	chr6:143014600-143017400	Weak transcription	Psoas Muscle	Psoas
30	chr6:143014600-143017800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr6:143014600-143018200	Enhancers	Muscle Satellite Cultured Cells	--
32	chr6:143014600-143018600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr6:143014600-143018600	Weak transcription	Brain Angular Gyrus	brain
34	chr6:143014600-143019000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr6:143014600-143023800	Weak transcription	Left Ventricle	heart
36	chr6:143014800-143015600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr6:143014800-143015800	Enhancers	Primary hematopoietic stem cells	blood
38	chr6:143014800-143015800	Weak transcription	Fetal Lung	lung
39	chr6:143014800-143016200	Weak transcription	Small Intestine	intestine
40	chr6:143014800-143017400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr6:143014800-143017600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr6:143014800-143017600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr6:143014800-143017800	Enhancers	NHDF-Ad	bronchial
44	chr6:143014800-143018600	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr6:143014800-143018600	Weak transcription	Fetal Thymus	thymus
46	chr6:143014800-143019000	Weak transcription	Placenta	Placenta
47	chr6:143015000-143015800	Enhancers	Primary monocytes fromperipheralblood	blood
48	chr6:143015000-143016000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr6:143015000-143017200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr6:143015000-143017800	Enhancers	NHLF	lung

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