Variant report

Variant	rs2129434
Chromosome Location	chr3:113138763-113138764
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 81 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10511326	0.94[CEU][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11916690	0.94[CEU][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.81[EUR][1000 genomes]
rs11921931	0.81[EUR][1000 genomes]
rs13064411	1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap]
rs13066742	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13083453	0.87[ASN][1000 genomes]
rs13086266	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13087452	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13098166	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13325046	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.84[MKK][hapmap];0.96[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1386336	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1486894	0.94[CEU][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.89[TSI][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1486897	0.94[CEU][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1552432	0.94[CEU][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs16860849	1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap]
rs16861103	0.83[TSI][hapmap]
rs16861158	0.90[CHD][hapmap];0.96[GIH][hapmap]
rs1872747	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2087129	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2291905	0.81[GIH][hapmap];0.91[MEX][hapmap]
rs2399477	0.83[TSI][hapmap]
rs2399479	0.94[CEU][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28536176	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28710051	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34049435	0.87[ASN][1000 genomes]
rs35860985	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs36054418	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3732803	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3773697	0.95[CHD][hapmap];0.96[GIH][hapmap];0.82[JPT][hapmap]
rs3829889	0.81[EUR][1000 genomes]
rs4396864	0.83[CEU][hapmap]
rs4425226	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4484165	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs60279293	0.87[ASN][1000 genomes]
rs6438149	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6438156	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6438157	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6438158	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6438159	0.94[CEU][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6438161	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs66866534	0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67211112	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6766615	0.94[CEU][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6768648	0.94[CEU][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6768979	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6769516	0.94[CEU][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6773497	0.94[CEU][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6778800	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6783965	0.94[CEU][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6786974	0.94[CEU][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6787026	1.00[CEU][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6798938	0.94[CEU][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6799610	0.94[CEU][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6808394	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs722392	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7610638	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7613546	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7619913	0.81[EUR][1000 genomes]
rs7622740	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7631082	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7631138	0.94[CEU][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7636128	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs775231	0.82[JPT][hapmap]
rs869342	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs869343	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9808893	0.94[CEU][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9814395	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9825827	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9835848	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9836396	0.94[CEU][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9839921	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9844447	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9851378	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9860549	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9869119	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9869318	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9872168	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9875025	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][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
rs2129434	BOC	cis	cerebellum	SCAN
rs2129434	BOC	cis	parietal	SCAN

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:113074400-113184400	Weak transcription	Hela-S3	cervix
2	chr3:113080800-113143800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr3:113099600-113144800	Weak transcription	Rectal Smooth Muscle	rectum
4	chr3:113102200-113148800	Weak transcription	Brain Angular Gyrus	brain
5	chr3:113102400-113144400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr3:113106800-113143600	Weak transcription	Dnd41	blood
7	chr3:113107200-113145200	Weak transcription	Aorta	Aorta
8	chr3:113109200-113159800	Weak transcription	Brain Hippocampus Middle	brain
9	chr3:113111600-113146400	Weak transcription	Brain Substantia Nigra	brain
10	chr3:113112200-113148400	Weak transcription	Brain Anterior Caudate	brain
11	chr3:113113000-113145600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr3:113114000-113143800	Weak transcription	Fetal Thymus	thymus
13	chr3:113117600-113148400	Weak transcription	Placenta	Placenta
14	chr3:113119600-113145200	Weak transcription	Lung	lung
15	chr3:113122400-113144800	Weak transcription	Pancreas	Pancrea
16	chr3:113122800-113144000	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr3:113122800-113144000	Weak transcription	Thymus	Thymus
18	chr3:113122800-113144800	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr3:113123000-113143600	Weak transcription	Left Ventricle	heart
20	chr3:113123000-113144400	Weak transcription	HSMM	muscle
21	chr3:113123200-113143800	Weak transcription	Ovary	ovary
22	chr3:113123600-113143200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr3:113124600-113143600	Weak transcription	Colon Smooth Muscle	Colon
24	chr3:113129000-113142600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr3:113132600-113146400	Weak transcription	Right Ventricle	heart
26	chr3:113133200-113147800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr3:113133400-113144600	Weak transcription	NH-A	brain
28	chr3:113134000-113144000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr3:113134000-113144400	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr3:113134200-113143600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr3:113134400-113143600	Weak transcription	Fetal Intestine Large	intestine
32	chr3:113134600-113144800	Weak transcription	Fetal Muscle Leg	muscle
33	chr3:113134600-113159800	Weak transcription	Fetal Muscle Trunk	muscle
34	chr3:113135000-113145600	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr3:113135200-113141600	Weak transcription	Primary hematopoietic stem cells	blood
36	chr3:113135200-113142200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr3:113135200-113143800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr3:113135200-113144000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr3:113135200-113144200	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr3:113135200-113144800	Weak transcription	Fetal Lung	lung
41	chr3:113135200-113164600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr3:113135400-113142000	Weak transcription	Primary T cells from cord blood	blood
43	chr3:113135400-113142200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr3:113135400-113143400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr3:113135400-113143800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr3:113135400-113143800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr3:113135400-113143800	Weak transcription	Primary T helper cells PMA-I stimulated	--
48	chr3:113135400-113143800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr3:113135400-113144000	Weak transcription	Adipose Nuclei	Adipose
50	chr3:113135400-113144400	Weak transcription	Fetal Kidney	kidney

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