Variant report

Variant	rs945309
Chromosome Location	chr14:70178981-70178982
allele	C/T
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr14:70160859..70163841-chr14:70176614..70179491,2	K562	blood:
2	chr14:70078043..70079983-chr14:70178508..70181365,3	MCF-7	breast:
3	chr14:70178635..70181592-chr14:70183298..70186714,3	K562	blood:
4	chr14:70129521..70131459-chr14:70177879..70180104,2	MCF-7	breast:
5	chr14:70163089..70166049-chr14:70176674..70179020,3	MCF-7	breast:
6	chr14:70114480..70116769-chr14:70178429..70180282,2	MCF-7	breast:
7	chr14:70175565..70179211-chr14:70180408..70183769,4	MCF-7	breast:
8	chr14:70076728..70078237-chr14:70177828..70179629,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000100647	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10149246	0.85[CHB][hapmap];0.85[CHD][hapmap];0.89[TSI][hapmap]
rs1275742	0.80[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1275745	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1275746	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1275817	0.88[CEU][hapmap];0.92[CHB][hapmap];0.91[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1275823	0.83[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs1290041	0.91[AFR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1295826	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1295827	1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17107161	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1743379	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1999722	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.87[GIH][hapmap];0.92[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2210803	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.92[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2332094	0.83[CHB][hapmap]
rs2766462	0.91[AFR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2766466	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34686932	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4902745	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55780993	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs60716885	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61980729	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61980730	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6573900	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7143960	0.80[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];0.91[ASN][1000 genomes]
rs7157093	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8006991	0.83[CHB][hapmap]
rs945308	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs945310	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs945312	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][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	nsv456336	chr14:70081956-70574149	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
2	nsv565007	chr14:70081956-70574149	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs945309	SLC8A3	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:70161600-70179200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr14:70163400-70179400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr14:70163400-70183400	Weak transcription	Hela-S3	cervix
4	chr14:70166600-70179000	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr14:70168200-70179200	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr14:70174200-70180200	Genic enhancers	Primary monocytes fromperipheralblood	blood
7	chr14:70174600-70179000	Strong transcription	Primary T killer memory cells from peripheral blood	blood
8	chr14:70175000-70179000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr14:70175000-70181600	Genic enhancers	Fetal Muscle Leg	muscle
10	chr14:70175200-70179200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr14:70175400-70180800	Enhancers	Brain Substantia Nigra	brain
12	chr14:70176000-70179600	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
13	chr14:70176000-70182000	Strong transcription	Primary B cells from peripheral blood	blood
14	chr14:70176200-70179200	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr14:70176400-70179000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr14:70176400-70179800	Transcr. at gene 5' and 3'	Monocytes-CD14+_RO01746	blood
17	chr14:70176600-70179000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr14:70176600-70179200	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
19	chr14:70176800-70180600	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr14:70177000-70180600	Genic enhancers	Placenta	Placenta
21	chr14:70177200-70179600	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr14:70177200-70180000	Genic enhancers	Rectal Mucosa Donor 31	rectum
23	chr14:70177200-70180400	Genic enhancers	Esophagus	oesophagus
24	chr14:70177200-70180800	Genic enhancers	Right Ventricle	heart
25	chr14:70177200-70181600	Genic enhancers	Fetal Thymus	thymus
26	chr14:70177200-70181600	Genic enhancers	Lung	lung
27	chr14:70177200-70184000	Enhancers	Skeletal Muscle Female	skeletal muscle
28	chr14:70177400-70179400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr14:70177400-70181400	Enhancers	Stomach Mucosa	stomach
30	chr14:70177400-70181600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr14:70177400-70181600	Genic enhancers	Fetal Intestine Small	intestine
32	chr14:70177400-70181600	Genic enhancers	Fetal Stomach	stomach
33	chr14:70177400-70182200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
34	chr14:70177400-70184200	Enhancers	Cortex derived primary cultured neurospheres	brain
35	chr14:70177600-70179600	Enhancers	ES-I3 Cell Line	embryonic stem cell
36	chr14:70177600-70179600	Genic enhancers	Gastric	stomach
37	chr14:70177600-70179800	Genic enhancers	GM12878-XiMat	blood
38	chr14:70177600-70180200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr14:70177600-70180400	Genic enhancers	Primary hematopoietic stem cells	blood
40	chr14:70177600-70180400	Enhancers	Brain Anterior Caudate	brain
41	chr14:70177600-70180400	Enhancers	Fetal Brain Female	brain
42	chr14:70177600-70180400	Enhancers	Right Atrium	heart
43	chr14:70177600-70180400	Genic enhancers	Sigmoid Colon	Sigmoid Colon
44	chr14:70177600-70181000	Genic enhancers	Fetal Intestine Large	intestine
45	chr14:70177600-70181400	Genic enhancers	Rectal Mucosa Donor 29	rectum
46	chr14:70177600-70181600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr14:70177600-70181600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr14:70177600-70181600	Genic enhancers	Fetal Muscle Trunk	muscle
49	chr14:70177600-70181800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
50	chr14:70177600-70182000	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood

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