Variant report

Variant	rs1474960
Chromosome Location	chr14:69129062-69129063
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr14:69127719..69129737-chr14:69289553..69291881,2	MCF-7	breast:
2	chr14:69125365..69129113-chr14:69131189..69133426,4	MCF-7	breast:
3	chr14:69128890..69132387-chr14:69257388..69259950,3	K562	blood:
4	chr14:69128588..69133050-chr14:69253079..69257196,5	MCF-7	breast:
5	chr14:69128066..69130361-chr14:69254081..69256689,3	MCF-7	breast:
6	chr14:69122826..69132436-chr14:69256721..69264610,21	MCF-7	breast:
7	chr14:69128118..69129295-chr14:69255476..69256194,4	MCF-7	breast:
8	chr14:68617419..68619958-chr14:69128377..69130233,2	MCF-7	breast:
9	chr14:69125361..69129179-chr14:69259239..69263742,5	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000185650	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10135342	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10873215	0.94[CEU][hapmap];0.83[TSI][hapmap]
rs11158755	0.93[CEU][hapmap]
rs17835218	0.83[CEU][hapmap];0.94[MEX][hapmap];0.96[TSI][hapmap];0.88[AMR][1000 genomes]
rs17835244	0.88[JPT][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2877496	0.88[CEU][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4899250	0.94[CEU][hapmap]
rs55767067	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7140554	0.83[CEU][hapmap]
rs7152224	0.83[CEU][hapmap]
rs8006890	0.88[CEU][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.83[EUR][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	esv1798800	chr14:69114353-69131030	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1474960	SIPA1L1	cis	parietal	SCAN
rs1474960	SLC39A9	cis	cerebellum	SCAN

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:69115400-69130200	Enhancers	Fetal Stomach	stomach
2	chr14:69120800-69139800	Enhancers	Fetal Muscle Leg	muscle
3	chr14:69121200-69129400	Enhancers	Placenta Amnion	Placenta Amnion
4	chr14:69122000-69136000	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr14:69122200-69131200	Weak transcription	Small Intestine	intestine
6	chr14:69122600-69129600	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr14:69122800-69133600	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr14:69122800-69133800	Weak transcription	Primary B cells from cord blood	blood
9	chr14:69123000-69129600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr14:69123000-69130600	Weak transcription	Liver	Liver
11	chr14:69123000-69137800	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr14:69123200-69131000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr14:69123800-69130400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr14:69124600-69130200	Enhancers	Placenta	Placenta
15	chr14:69124800-69131800	Enhancers	Spleen	Spleen
16	chr14:69126000-69130000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr14:69126400-69129400	Weak transcription	NH-A	brain
18	chr14:69126400-69129400	Weak transcription	Osteobl	bone
19	chr14:69126600-69129200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr14:69126600-69129200	Weak transcription	Brain Cingulate Gyrus	brain
21	chr14:69126600-69129200	Weak transcription	Colonic Mucosa	Colon
22	chr14:69126600-69130000	Weak transcription	Adipose Nuclei	Adipose
23	chr14:69126600-69130000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr14:69126600-69130200	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr14:69126600-69130200	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr14:69126600-69131000	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr14:69126600-69131200	Weak transcription	Brain Anterior Caudate	brain
28	chr14:69126600-69131400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr14:69126600-69133000	Weak transcription	Gastric	stomach
30	chr14:69126600-69135000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr14:69126600-69136000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr14:69126800-69129200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr14:69126800-69130000	Weak transcription	Duodenum Mucosa	Duodenum
34	chr14:69126800-69131000	Weak transcription	Fetal Kidney	kidney
35	chr14:69126800-69131200	Weak transcription	Esophagus	oesophagus
36	chr14:69126800-69131200	Weak transcription	Right Atrium	heart
37	chr14:69126800-69131800	Weak transcription	Fetal Intestine Large	intestine
38	chr14:69127000-69131200	Weak transcription	Fetal Intestine Small	intestine
39	chr14:69127000-69132400	Weak transcription	Fetal Thymus	thymus
40	chr14:69127400-69129600	Weak transcription	Rectal Smooth Muscle	rectum
41	chr14:69127400-69133600	Weak transcription	Pancreas	Pancrea
42	chr14:69127800-69131200	Weak transcription	Left Ventricle	heart
43	chr14:69128000-69130000	Weak transcription	Stomach Smooth Muscle	stomach
44	chr14:69128000-69130000	Enhancers	HSMMtube	muscle
45	chr14:69128000-69134400	Enhancers	Fetal Heart	heart
46	chr14:69128200-69129200	Weak transcription	GM12878-XiMat	blood
47	chr14:69128200-69130000	Enhancers	HSMM	muscle
48	chr14:69128200-69130200	Weak transcription	Ovary	ovary
49	chr14:69128200-69131800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr14:69128400-69129800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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