Variant report

Variant	rs3950069
Chromosome Location	chr14:68852875-68852876
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EP300	chr14:68852497-68854798	SK-N-SH	brain:	n/a	chr14:68854401-68854415 chr14:68854215-68854225 chr14:68854106-68854120

No.	Distal block	Cell Line	Cell type
1	chr14:68850065..68853028-chr14:68854174..68855948,2	MCF-7	breast:
2	chr14:68846943..68849036-chr14:68850904..68853238,2	MCF-7	breast:
3	chr14:68849279..68853036-chr14:68925939..68929072,3	MCF-7	breast:
4	chr14:68852547..68854208-chr14:69260882..69263512,3	MCF-7	breast:

Variant related genes	Relation type
RAD51B	TF binding region
ENSG00000185650	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1006816	0.86[JPT][hapmap]
rs11158732	0.88[CEU][hapmap]
rs11625452	0.85[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.83[TSI][hapmap]
rs11627490	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11628653	0.85[CEU][hapmap];0.89[MEX][hapmap]
rs12889666	0.83[JPT][hapmap]
rs1885014	0.92[ASW][hapmap];1.00[CEU][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1956537	0.85[CHD][hapmap];0.87[JPT][hapmap]
rs1977211	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2009721	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs2208396	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2331693	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs2331696	0.81[CHB][hapmap];0.95[JPT][hapmap]
rs2877461	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3784113	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs3784115	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3784116	0.83[JPT][hapmap]
rs3784119	0.81[CHB][hapmap];0.95[JPT][hapmap]
rs3784120	0.85[CHD][hapmap];0.87[JPT][hapmap]
rs55749276	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs58339869	0.95[EUR][1000 genomes]
rs59993918	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61039700	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61986905	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61986906	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs61986910	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8013236	0.80[CEU][hapmap]
rs8014025	0.89[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.89[MEX][hapmap];0.82[MKK][hapmap];0.91[TSI][hapmap]
rs8014234	0.88[CEU][hapmap];0.85[CHB][hapmap];0.89[JPT][hapmap]
rs8018477	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8021199	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869154	chr14:68366754-69041768	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3950069	MED6	cis	cerebellum	SCAN
rs3950069	DCAF5	cis	parietal	SCAN
rs3950069	CHURC1	cis	parietal	SCAN

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:68844600-68858000	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr14:68844600-68859200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr14:68844800-68853000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr14:68845200-68853200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr14:68845200-68853600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr14:68845200-68858800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr14:68845800-68853200	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr14:68847600-68859000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr14:68847600-68862600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr14:68848000-68853800	Weak transcription	Osteobl	bone
11	chr14:68848200-68856600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr14:68848800-68857200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr14:68849400-68854600	Enhancers	Primary monocytes fromperipheralblood	blood
14	chr14:68850000-68855800	Enhancers	Rectal Smooth Muscle	rectum
15	chr14:68850200-68853800	Weak transcription	Liver	Liver
16	chr14:68850200-68861000	Enhancers	Colon Smooth Muscle	Colon
17	chr14:68850400-68854000	Enhancers	Skeletal Muscle Female	skeletal muscle
18	chr14:68850400-68854600	Enhancers	Fetal Heart	heart
19	chr14:68850400-68857600	Weak transcription	Small Intestine	intestine
20	chr14:68850800-68853200	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr14:68850800-68853200	Weak transcription	Brain Substantia Nigra	brain
22	chr14:68850800-68853200	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr14:68850800-68853400	Weak transcription	Aorta	Aorta
24	chr14:68850800-68853600	Weak transcription	Primary T cells from cord blood	blood
25	chr14:68850800-68859000	Weak transcription	Primary B cells from peripheral blood	blood
26	chr14:68851200-68853600	Enhancers	Spleen	Spleen
27	chr14:68851400-68853200	Weak transcription	A549	lung
28	chr14:68851400-68853800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr14:68851400-68854200	Weak transcription	GM12878-XiMat	blood
30	chr14:68851400-68854600	Enhancers	Fetal Lung	lung
31	chr14:68851400-68857400	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr14:68851800-68853000	Weak transcription	Fetal Kidney	kidney
33	chr14:68851800-68853800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr14:68851800-68858000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr14:68851800-68858400	Weak transcription	Fetal Intestine Large	intestine
36	chr14:68851800-68858800	Weak transcription	Duodenum Mucosa	Duodenum
37	chr14:68851800-68859000	Weak transcription	Primary B cells from cord blood	blood
38	chr14:68851800-68859800	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr14:68851800-68861000	Weak transcription	Stomach Mucosa	stomach
40	chr14:68852000-68853000	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr14:68852000-68853000	Weak transcription	Fetal Brain Female	brain
42	chr14:68852000-68853200	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr14:68852000-68853200	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr14:68852000-68853200	Weak transcription	Ovary	ovary
45	chr14:68852000-68853400	Weak transcription	Psoas Muscle	Psoas
46	chr14:68852000-68853800	Weak transcription	Primary hematopoietic stem cells	blood
47	chr14:68852000-68853800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr14:68852000-68853800	Weak transcription	HMEC	breast
49	chr14:68852000-68857000	Weak transcription	NHDF-Ad	bronchial
50	chr14:68852000-68857800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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