Variant report

Variant	rs2025009
Chromosome Location	chr14:68843605-68843606
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:68842793..68845023-chr14:69283063..69285593,2	K562	blood:
2	chr14:68841263..68843280-chr14:68843376..68844919,2	MCF-7	breast:
3	chr14:68843051..68845983-chr14:68924155..68927430,4	MCF-7	breast:
4	chr14:68843357..68844886-chr14:68924790..68926556,2	MCF-7	breast:

Extended variants
information (count: 20 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1006816	0.82[CHB][hapmap]
rs11627490	0.81[ASN][1000 genomes]
rs1885014	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.97[ASN][1000 genomes]
rs1956537	0.82[CHB][hapmap];0.84[CHD][hapmap]
rs1977211	0.95[ASN][1000 genomes]
rs2009721	0.93[ASN][1000 genomes]
rs2331693	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2331696	0.87[CEU][hapmap]
rs2877461	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.97[ASN][1000 genomes]
rs3784113	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs3784115	0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.97[ASN][1000 genomes]
rs3784119	0.96[CEU][hapmap];0.86[TSI][hapmap]
rs3784120	0.82[CHB][hapmap];0.84[CHD][hapmap]
rs55749276	0.95[ASN][1000 genomes]
rs58339869	0.96[ASN][1000 genomes]
rs61986906	0.94[ASN][1000 genomes]
rs61986910	0.97[ASN][1000 genomes]
rs8018477	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.97[ASN][1000 genomes]
rs927221	0.83[CHD][hapmap];0.86[JPT][hapmap];0.82[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
rs2025009	SYNJ2BP	cis	parietal	SCAN
rs2025009	CHURC1	cis	parietal	SCAN
rs2025009	HAS2	trans	cerebellum	SCAN

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:68831800-68844200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr14:68832000-68843800	Weak transcription	Ovary	ovary
3	chr14:68832000-68844200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr14:68832000-68851600	Weak transcription	Lung	lung
5	chr14:68832200-68844200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr14:68832200-68844200	Weak transcription	Brain Germinal Matrix	brain
7	chr14:68833000-68845200	Enhancers	Primary B cells from peripheral blood	blood
8	chr14:68834400-68846400	Weak transcription	Fetal Heart	heart
9	chr14:68835600-68843800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr14:68836400-68847000	Weak transcription	Aorta	Aorta
11	chr14:68836800-68843800	Weak transcription	Duodenum Mucosa	Duodenum
12	chr14:68837400-68844000	Weak transcription	Stomach Mucosa	stomach
13	chr14:68839200-68844200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr14:68839400-68844200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr14:68839600-68844000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr14:68839800-68844000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr14:68839800-68844000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr14:68839800-68844200	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr14:68839800-68850600	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr14:68840000-68845800	Enhancers	Primary monocytes fromperipheralblood	blood
21	chr14:68840400-68844200	Enhancers	Primary B cells from cord blood	blood
22	chr14:68840600-68847600	Enhancers	Primary T helper cells PMA-I stimulated	--
23	chr14:68840600-68847800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
24	chr14:68840800-68844600	Enhancers	Fetal Muscle Leg	muscle
25	chr14:68840800-68845200	Enhancers	Skeletal Muscle Female	skeletal muscle
26	chr14:68840800-68847400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
27	chr14:68840800-68847400	Enhancers	Primary T helper cells fromperipheralblood	blood
28	chr14:68840800-68847600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
29	chr14:68840800-68847600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
30	chr14:68841000-68844600	Enhancers	Fetal Thymus	thymus
31	chr14:68841000-68846000	Enhancers	Fetal Lung	lung
32	chr14:68841200-68844000	Enhancers	GM12878-XiMat	blood
33	chr14:68841200-68845800	Enhancers	Cortex derived primary cultured neurospheres	brain
34	chr14:68841400-68844600	Enhancers	Primary T cells fromperipheralblood	blood
35	chr14:68841400-68845200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr14:68841400-68845200	Enhancers	Rectal Smooth Muscle	rectum
37	chr14:68841400-68847200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
38	chr14:68841600-68844000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr14:68841600-68844200	Enhancers	Psoas Muscle	Psoas
40	chr14:68841600-68844200	Weak transcription	A549	lung
41	chr14:68841600-68845400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr14:68841800-68844000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr14:68841800-68844000	Weak transcription	Fetal Brain Female	brain
44	chr14:68842000-68844200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr14:68842000-68844600	Enhancers	Thymus	Thymus
46	chr14:68842000-68845200	Enhancers	Primary T killer memory cells from peripheral blood	blood
47	chr14:68842000-68845200	Enhancers	Skeletal Muscle Male	skeletal muscle
48	chr14:68842000-68845800	Enhancers	Primary T helper naive cells from peripheral blood	blood
49	chr14:68842200-68845200	Enhancers	Breast Myoepithelial Primary Cells	Breast
50	chr14:68842400-68844200	Weak transcription	HUES6 Cell Line	embryonic stem cell

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