Variant report

Variant	rs6438144
Chromosome Location	chr3:113123328-113123329
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10934228	0.89[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.90[AMR][1000 genomes]
rs11715198	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12488964	0.96[CEU][hapmap];0.92[CHD][hapmap];0.89[GIH][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12635786	0.87[CHB][hapmap]
rs12636607	0.86[CHB][hapmap]
rs13091945	0.83[AMR][1000 genomes]
rs17321330	0.92[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];0.81[GIH][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap]
rs1906142	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1979554	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2054823	1.00[ASW][hapmap];0.96[CEU][hapmap];0.92[CHD][hapmap];0.89[GIH][hapmap];0.94[LWK][hapmap];0.95[MEX][hapmap];0.80[MKK][hapmap];0.91[TSI][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2129430	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2171293	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2895413	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35581027	0.87[EUR][1000 genomes]
rs35935366	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3732806	0.87[CHB][hapmap]
rs4682138	0.83[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4682486	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6438140	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6438143	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6438145	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6438146	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6438147	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6438148	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs66524865	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6768117	0.83[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6769970	0.80[CEU][hapmap];0.82[CHB][hapmap];0.86[YRI][hapmap]
rs6775574	1.00[ASW][hapmap];0.96[CEU][hapmap];0.92[CHD][hapmap];0.89[GIH][hapmap];0.97[LWK][hapmap];0.95[MEX][hapmap];0.82[MKK][hapmap];0.91[TSI][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6777880	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6805691	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7617772	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7618884	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7621210	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7623122	0.83[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7623389	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7625841	1.00[ASW][hapmap];0.96[CEU][hapmap];0.92[CHD][hapmap];0.89[GIH][hapmap];0.97[LWK][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];0.91[TSI][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7631730	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7633428	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7642163	0.85[EUR][1000 genomes]
rs7643592	0.83[MEX][hapmap];0.82[TSI][hapmap]
rs7643843	0.83[MEX][hapmap];0.82[TSI][hapmap]
rs7646985	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7647220	0.82[TSI][hapmap]
rs7650538	0.96[CEU][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs775232	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs775233	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9682734	1.00[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9815835	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9840124	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9848087	1.00[ASW][hapmap];0.96[CEU][hapmap];0.92[CHD][hapmap];0.89[GIH][hapmap];0.86[LWK][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];0.91[TSI][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9866748	0.96[CEU][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9869141	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9870996	0.82[YRI][hapmap]
rs9990291	0.84[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3431441	chr3:112453467-113213252	Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv1013506	chr3:112890608-113680951	Weak transcription Bivalent/Poised TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv1004000	chr3:113116778-113513899	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6438144	SIDT1	cis	parietal	SCAN
rs6438144	WDR52	cis	parietal	SCAN

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:113074400-113184400	Weak transcription	Hela-S3	cervix
2	chr3:113080000-113123800	Weak transcription	Primary B cells from peripheral blood	blood
3	chr3:113080800-113143800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr3:113092400-113134200	Weak transcription	Fetal Kidney	kidney
5	chr3:113093600-113134800	Weak transcription	Primary T helper cells PMA-I stimulated	--
6	chr3:113098800-113134800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr3:113099000-113134800	Weak transcription	A549	lung
8	chr3:113099600-113144800	Weak transcription	Rectal Smooth Muscle	rectum
9	chr3:113102200-113148800	Weak transcription	Brain Angular Gyrus	brain
10	chr3:113102400-113144400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr3:113103200-113126200	Weak transcription	Right Ventricle	heart
12	chr3:113104000-113127400	Weak transcription	Duodenum Mucosa	Duodenum
13	chr3:113105600-113124200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr3:113106800-113143600	Weak transcription	Dnd41	blood
15	chr3:113107000-113127400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr3:113107000-113137000	Weak transcription	Esophagus	oesophagus
17	chr3:113107200-113124200	Weak transcription	Fetal Stomach	stomach
18	chr3:113107200-113124200	Weak transcription	GM12878-XiMat	blood
19	chr3:113107200-113124600	Weak transcription	Fetal Intestine Small	intestine
20	chr3:113107200-113145200	Weak transcription	Aorta	Aorta
21	chr3:113107600-113138200	Weak transcription	Monocytes-CD14+_RO01746	blood
22	chr3:113108600-113125000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr3:113109200-113159800	Weak transcription	Brain Hippocampus Middle	brain
24	chr3:113110200-113124400	Weak transcription	Fetal Muscle Trunk	muscle
25	chr3:113111600-113146400	Weak transcription	Brain Substantia Nigra	brain
26	chr3:113112200-113148400	Weak transcription	Brain Anterior Caudate	brain
27	chr3:113112800-113123800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr3:113113000-113145600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr3:113114000-113143800	Weak transcription	Fetal Thymus	thymus
30	chr3:113114200-113123800	Weak transcription	Small Intestine	intestine
31	chr3:113116000-113125200	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr3:113117400-113128000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr3:113117600-113148400	Weak transcription	Placenta	Placenta
34	chr3:113118000-113134800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr3:113118200-113124400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr3:113118200-113124400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr3:113118200-113124400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr3:113119200-113124000	Weak transcription	Adipose Nuclei	Adipose
39	chr3:113119400-113129600	Weak transcription	Psoas Muscle	Psoas
40	chr3:113119600-113145200	Weak transcription	Lung	lung
41	chr3:113120000-113124400	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr3:113121200-113123800	Strong transcription	Rectal Mucosa Donor 29	rectum
43	chr3:113121200-113124400	Strong transcription	Liver	Liver
44	chr3:113121200-113125000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
45	chr3:113121400-113123400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr3:113121400-113128600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr3:113121600-113134600	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr3:113121800-113123600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr3:113122200-113124400	Weak transcription	Brain Cingulate Gyrus	brain
50	chr3:113122200-113125400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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