Variant report

Variant	rs1894709
Chromosome Location	chr1:175132371-175132372
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:175130416..175133379-chr1:175161541..175164085,2	MCF-7	breast:
2	chr1:175127835..175129941-chr1:175131932..175135022,3	K562	blood:

Variant related genes	Relation type
ENSG00000235750	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1014554	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1014555	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10489326	0.85[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.92[MKK][hapmap];0.88[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1057239	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[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];1.00[ASN][1000 genomes]
rs1057246	0.87[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.98[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1057302	0.81[CEU][hapmap];0.85[CHB][hapmap];0.82[GIH][hapmap];0.89[MEX][hapmap]
rs1057305	0.85[CEU][hapmap];0.85[CHB][hapmap]
rs10753091	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10912901	1.00[CEU][hapmap];0.84[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11583687	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11585368	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12760073	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13373754	0.93[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13374887	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1883102	0.89[AFR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2272784	0.94[ASW][hapmap]
rs2285216	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2285219	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2285220	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2685	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34270511	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34370567	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[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]
rs3753555	0.94[ASW][hapmap]
rs3766685	0.87[ASW][hapmap]
rs3766688	0.88[ASW][hapmap]
rs4344281	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4650716	0.85[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.92[MKK][hapmap];0.89[TSI][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6664840	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6929	0.85[CEU][hapmap];0.87[GIH][hapmap];0.90[MEX][hapmap]
rs729675	0.89[AFR][1000 genomes];0.88[EUR][1000 genomes];0.96[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	nsv522101	chr1:175109517-175151183	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv429924	chr1:175110480-175134314	Enhancers Bivalent/Poised TSS Strong transcription Weak transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1894709	KIAA0040	Cis_1M	lymphoblastoid	RTeQTL
rs1894709	KIAA0040	cis	multi-tissue	Pritchard

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:175120000-175139400	Weak transcription	Colon Smooth Muscle	Colon
2	chr1:175122200-175132800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr1:175122200-175133400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr1:175122200-175136600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr1:175124000-175140400	Weak transcription	Fetal Heart	heart
6	chr1:175124400-175138200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr1:175124600-175134600	Weak transcription	Small Intestine	intestine
8	chr1:175125400-175132400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr1:175126800-175138200	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr1:175126800-175141800	Strong transcription	Primary B cells from cord blood	blood
11	chr1:175126800-175148800	Strong transcription	Primary monocytes fromperipheralblood	blood
12	chr1:175127000-175135600	Strong transcription	Duodenum Mucosa	Duodenum
13	chr1:175127000-175136200	Strong transcription	Thymus	Thymus
14	chr1:175127000-175136600	Strong transcription	Primary neutrophils fromperipheralblood	blood
15	chr1:175127000-175136600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr1:175127000-175148400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr1:175127200-175136200	Strong transcription	Fetal Thymus	thymus
18	chr1:175127200-175137800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr1:175127200-175139000	Strong transcription	Primary B cells from peripheral blood	blood
20	chr1:175127200-175139000	Strong transcription	Placenta	Placenta
21	chr1:175127200-175139200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr1:175127200-175147800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr1:175127400-175134400	Weak transcription	Brain Substantia Nigra	brain
24	chr1:175127400-175137000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr1:175127400-175139200	Strong transcription	Primary T cells fromperipheralblood	blood
26	chr1:175127400-175144200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
27	chr1:175127400-175149400	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr1:175127600-175132400	Strong transcription	Adipose Nuclei	Adipose
29	chr1:175127600-175132600	Strong transcription	Left Ventricle	heart
30	chr1:175127600-175133000	Strong transcription	Stomach Smooth Muscle	stomach
31	chr1:175127600-175136600	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr1:175127600-175136800	Strong transcription	Sigmoid Colon	Sigmoid Colon
33	chr1:175127600-175137200	Strong transcription	Pancreas	Pancrea
34	chr1:175127600-175137600	Strong transcription	Primary T helper cells fromperipheralblood	blood
35	chr1:175127600-175137600	Strong transcription	Liver	Liver
36	chr1:175127600-175140600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr1:175127800-175136000	Strong transcription	Lung	lung
38	chr1:175127800-175136400	Strong transcription	Skeletal Muscle Male	skeletal muscle
39	chr1:175127800-175139200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr1:175127800-175140200	Strong transcription	Spleen	Spleen
41	chr1:175128200-175135000	Strong transcription	Aorta	Aorta
42	chr1:175128200-175137000	Strong transcription	Rectal Mucosa Donor 31	rectum
43	chr1:175128200-175138400	Strong transcription	Primary T helper cells PMA-I stimulated	--
44	chr1:175128200-175140000	Strong transcription	Primary T cells from cord blood	blood
45	chr1:175128400-175132800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr1:175128400-175136000	Strong transcription	Ovary	ovary
47	chr1:175128400-175136000	Strong transcription	Skeletal Muscle Female	skeletal muscle
48	chr1:175128400-175138800	Strong transcription	GM12878-XiMat	blood
49	chr1:175128400-175139200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr1:175128600-175136600	Strong transcription	HMEC	breast

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