Variant report

Variant	rs6440003
Chromosome Location	chr3:141094209-141094210
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:141092073..141094472-chr3:141095647..141097319,2	MCF-7	breast:
2	chr3:141083461..141090540-chr3:141091667..141099186,10	MCF-7	breast:
3	chr3:141091576..141094274-chr3:141094633..141097047,3	K562	blood:
4	chr3:141091576..141094274-chr3:141094633..141096791,2	K562	blood:

Variant related genes	Relation type
ENSG00000249417	Chromatin interaction
ENSG00000177311	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs13068733	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13077048	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1344672	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1344674	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1346408	0.81[CEU][hapmap]
rs1582874	1.00[CEU][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1863868	0.81[CEU][hapmap];0.81[JPT][hapmap]
rs1991431	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2871960	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4683605	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4683606	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57345461	0.95[ASN][1000 genomes]
rs58473751	0.95[ASN][1000 genomes]
rs6440006	0.96[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6762826	0.90[JPT][hapmap]
rs6763927	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6763931	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6764769	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6785012	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6802753	0.84[JPT][hapmap]
rs6808936	1.00[CEU][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs724016	0.91[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7613516	0.81[CEU][hapmap]
rs7624084	0.89[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7625643	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7632381	0.90[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7650602	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9846396	1.00[CEU][hapmap];0.82[GIH][hapmap];0.96[MEX][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9853018	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9856584	0.81[CHB][hapmap];1.00[JPT][hapmap];0.86[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	nsv829744	chr3:141016749-141189168	Genic enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

Variant related diseases (count:2)

Disease	PMID	Source
Height	18391952	GWAS catalog
Height	21998595	GWAS catalog

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6440003	ZBTB38	cis	cerebellum	SCAN
rs6440003	SPSB4	cis	parietal	SCAN
rs6440003	RASA2	cis	cerebellum	SCAN

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:141087000-141107800	Weak transcription	Pancreas	Pancrea
2	chr3:141088000-141102400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr3:141088000-141105200	Weak transcription	Fetal Muscle Trunk	muscle
4	chr3:141088200-141094400	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr3:141088200-141095000	Weak transcription	Colonic Mucosa	Colon
6	chr3:141088200-141101800	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr3:141088200-141102400	Weak transcription	Fetal Kidney	kidney
8	chr3:141088400-141102400	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr3:141088400-141107600	Weak transcription	Small Intestine	intestine
10	chr3:141089000-141094600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr3:141089200-141094400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr3:141089200-141094400	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr3:141089200-141094400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr3:141089200-141094600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr3:141089200-141095000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr3:141089200-141095200	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr3:141089200-141096200	Weak transcription	Fetal Lung	lung
18	chr3:141089200-141097600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr3:141089200-141097600	Weak transcription	Adipose Nuclei	Adipose
20	chr3:141089200-141098800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr3:141089200-141099000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr3:141089200-141101800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr3:141089200-141101800	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr3:141089200-141104800	Strong transcription	Fetal Intestine Large	intestine
25	chr3:141089200-141115800	Weak transcription	Psoas Muscle	Psoas
26	chr3:141089400-141094600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr3:141089400-141102200	Weak transcription	Stomach Smooth Muscle	stomach
28	chr3:141089400-141104200	Weak transcription	Fetal Muscle Leg	muscle
29	chr3:141089600-141094400	Weak transcription	Primary B cells from peripheral blood	blood
30	chr3:141089600-141094800	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr3:141089600-141096000	Genic enhancers	A549	lung
32	chr3:141089600-141099000	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr3:141089600-141102400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr3:141089600-141102400	Weak transcription	Fetal Brain Male	brain
35	chr3:141089600-141102400	Weak transcription	Rectal Smooth Muscle	rectum
36	chr3:141089600-141105600	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr3:141089800-141094600	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr3:141089800-141094600	Weak transcription	HUVEC	blood vessel
39	chr3:141089800-141097600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr3:141089800-141097800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr3:141089800-141099200	Weak transcription	Brain Anterior Caudate	brain
42	chr3:141089800-141099800	Weak transcription	Brain Angular Gyrus	brain
43	chr3:141089800-141102600	Strong transcription	Fetal Intestine Small	intestine
44	chr3:141090600-141094400	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr3:141091000-141107200	Weak transcription	Liver	Liver
46	chr3:141091200-141094400	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr3:141091400-141095200	Enhancers	ES-I3 Cell Line	embryonic stem cell
48	chr3:141091400-141095200	Enhancers	HUES6 Cell Line	embryonic stem cell
49	chr3:141091600-141094600	Enhancers	HUES64 Cell Line	embryonic stem cell
50	chr3:141091600-141095200	Enhancers	iPS-18 Cell Line	embryonic stem cell

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