Variant report

Variant	rs6438143
Chromosome Location	chr3:113117829-113117830
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10934228	0.80[JPT][hapmap];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11715198	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12488964	0.96[CEU][hapmap];0.81[CHB][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12635786	0.86[CHB][hapmap]
rs12636607	0.82[CHB][hapmap]
rs13091945	0.83[AMR][1000 genomes]
rs17321330	0.92[CEU][hapmap];0.85[CHB][hapmap]
rs1906142	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1979554	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2054823	0.95[CEU][hapmap];0.81[CHB][hapmap];0.94[YRI][hapmap];0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2129430	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2171293	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2895413	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35581027	0.86[EUR][1000 genomes]
rs35935366	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3732806	0.82[CHB][hapmap]
rs4682138	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4682486	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6438140	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6438144	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	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6438146	0.96[AMR][1000 genomes];0.99[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];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6438148	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs66524865	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6768117	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6769970	0.86[CHB][hapmap];0.90[YRI][hapmap]
rs6775574	0.96[CEU][hapmap];0.81[CHB][hapmap];0.94[YRI][hapmap];0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6777880	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6805201	0.92[CEU][hapmap]
rs6805691	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7617772	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7618884	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7621210	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7623122	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7623389	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7625841	0.96[CEU][hapmap];0.94[YRI][hapmap];0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7631730	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7633428	0.90[CHB][hapmap];0.85[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7642163	0.84[EUR][1000 genomes]
rs7643592	0.91[CEU][hapmap]
rs7643843	0.91[CEU][hapmap]
rs7646985	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7647220	0.87[CEU][hapmap]
rs7650538	0.96[CEU][hapmap];0.81[CHB][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7653186	0.92[CEU][hapmap]
rs775232	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs775233	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9682734	1.00[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9815835	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9840124	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9848087	0.96[CEU][hapmap];0.80[CHB][hapmap];0.94[YRI][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9866748	0.96[CEU][hapmap];0.81[CHB][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9869141	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9874749	0.92[CEU][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6438143	SIDT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:80 , 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	chr3:113081600-113121200	Weak transcription	Ovary	ovary
5	chr3:113081600-113121200	Weak transcription	Pancreas	Pancrea
6	chr3:113090800-113121200	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr3:113092400-113134200	Weak transcription	Fetal Kidney	kidney
8	chr3:113093600-113134800	Weak transcription	Primary T helper cells PMA-I stimulated	--
9	chr3:113096600-113121200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr3:113098800-113134800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr3:113099000-113134800	Weak transcription	A549	lung
12	chr3:113099600-113144800	Weak transcription	Rectal Smooth Muscle	rectum
13	chr3:113101800-113121200	Weak transcription	Primary hematopoietic stem cells	blood
14	chr3:113102200-113148800	Weak transcription	Brain Angular Gyrus	brain
15	chr3:113102400-113144400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr3:113102800-113122600	Weak transcription	Spleen	Spleen
17	chr3:113103200-113126200	Weak transcription	Right Ventricle	heart
18	chr3:113104000-113127400	Weak transcription	Duodenum Mucosa	Duodenum
19	chr3:113105200-113122000	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr3:113105600-113124200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr3:113106800-113122000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr3:113106800-113143600	Weak transcription	Dnd41	blood
23	chr3:113107000-113121800	Weak transcription	Fetal Intestine Large	intestine
24	chr3:113107000-113127400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr3:113107000-113137000	Weak transcription	Esophagus	oesophagus
26	chr3:113107200-113122000	Weak transcription	Gastric	stomach
27	chr3:113107200-113124200	Weak transcription	Fetal Stomach	stomach
28	chr3:113107200-113124200	Weak transcription	GM12878-XiMat	blood
29	chr3:113107200-113124600	Weak transcription	Fetal Intestine Small	intestine
30	chr3:113107200-113145200	Weak transcription	Aorta	Aorta
31	chr3:113107600-113138200	Weak transcription	Monocytes-CD14+_RO01746	blood
32	chr3:113108600-113125000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr3:113109200-113159800	Weak transcription	Brain Hippocampus Middle	brain
34	chr3:113109400-113121800	Weak transcription	Fetal Lung	lung
35	chr3:113110200-113124400	Weak transcription	Fetal Muscle Trunk	muscle
36	chr3:113110600-113121200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr3:113111200-113122000	Weak transcription	HSMM	muscle
38	chr3:113111600-113146400	Weak transcription	Brain Substantia Nigra	brain
39	chr3:113112000-113122200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr3:113112200-113148400	Weak transcription	Brain Anterior Caudate	brain
41	chr3:113112400-113121400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr3:113112400-113123200	Strong transcription	Primary T cells from cord blood	blood
43	chr3:113112800-113123800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr3:113113000-113145600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr3:113113200-113121200	Weak transcription	Brain Cingulate Gyrus	brain
46	chr3:113113200-113122600	Weak transcription	Primary monocytes fromperipheralblood	blood
47	chr3:113113600-113119600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr3:113114000-113143800	Weak transcription	Fetal Thymus	thymus
49	chr3:113114200-113123800	Weak transcription	Small Intestine	intestine
50	chr3:113116000-113118600	Strong transcription	Sigmoid Colon	Sigmoid Colon

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