Variant report

Variant	rs12741940
Chromosome Location	chr1:175908200-175908201
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10494495	0.91[JPT][hapmap]
rs10753117	0.86[JPT][hapmap]
rs10798425	0.91[JPT][hapmap]
rs10798434	0.91[JPT][hapmap]
rs10798442	0.86[JPT][hapmap]
rs10913117	0.91[JPT][hapmap]
rs10913118	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10913135	0.81[JPT][hapmap]
rs10913137	0.82[JPT][hapmap]
rs11810706	0.95[CEU][hapmap];0.91[JPT][hapmap];0.94[TSI][hapmap];0.83[EUR][1000 genomes]
rs12029090	0.84[JPT][hapmap]
rs12033847	0.86[JPT][hapmap]
rs12135395	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12138008	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes]
rs12404596	0.86[JPT][hapmap]
rs12723724	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12729524	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes]
rs12756741	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16849486	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17354120	0.82[JPT][hapmap]
rs2481628	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs2481630	1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap]
rs2481631	1.00[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap]
rs2481633	1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap]
rs2481646	0.82[AMR][1000 genomes]
rs2481655	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes]
rs2502823	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes]
rs2502829	0.82[AMR][1000 genomes]
rs2502831	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs2502845	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap]
rs34973462	0.83[EUR][1000 genomes]
rs3934392	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4409605	0.91[JPT][hapmap]
rs6660080	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6678628	0.82[JPT][hapmap]
rs6678812	0.82[JPT][hapmap]
rs6682194	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7517503	0.82[JPT][hapmap]
rs7530719	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7549160	0.90[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.84[AMR][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	esv33328	chr1:175446583-175910001	Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	esv1823794	chr1:175869554-176311778	Enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12741940	VAMP4	cis	parietal	SCAN
rs12741940	EME2	trans	cerebellum	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:175874400-175945600	Weak transcription	A549	lung
2	chr1:175880000-175937800	Weak transcription	HSMMtube	muscle
3	chr1:175881000-175924200	Weak transcription	Brain Angular Gyrus	brain
4	chr1:175882600-175910200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr1:175883200-175908200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr1:175886400-175929400	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr1:175887800-175929800	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr1:175889200-175937800	Weak transcription	Osteobl	bone
9	chr1:175891400-175908800	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr1:175892000-175908800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr1:175892400-175940600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr1:175893200-175943000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr1:175895200-175908800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr1:175895800-175908800	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr1:175897000-175953000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr1:175897200-175908800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr1:175897600-175908400	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr1:175897600-175908800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr1:175897600-175909200	Weak transcription	Brain Germinal Matrix	brain
20	chr1:175897600-175911000	Weak transcription	Thymus	Thymus
21	chr1:175897600-175953200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr1:175897800-175952400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr1:175898400-175909000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr1:175898600-175953200	Weak transcription	Pancreas	Pancrea
25	chr1:175898800-175909000	Weak transcription	Left Ventricle	heart
26	chr1:175899000-175908800	Weak transcription	Fetal Intestine Large	intestine
27	chr1:175899200-175953200	Weak transcription	Esophagus	oesophagus
28	chr1:175900800-175908400	Weak transcription	Dnd41	blood
29	chr1:175901400-175908600	Weak transcription	Primary T helper cells fromperipheralblood	blood
30	chr1:175901600-175940600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr1:175901800-175925800	Weak transcription	HUVEC	blood vessel
32	chr1:175902400-175914800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr1:175902400-175917800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr1:175902600-175909000	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr1:175902800-175931800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr1:175903200-175909200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr1:175903200-175924200	Weak transcription	Gastric	stomach
38	chr1:175903400-175951400	Weak transcription	K562	blood
39	chr1:175903600-175909000	Weak transcription	Duodenum Mucosa	Duodenum
40	chr1:175903600-175940800	Weak transcription	HMEC	breast
41	chr1:175903800-175908600	Weak transcription	Placenta	Placenta
42	chr1:175903800-175915800	Weak transcription	GM12878-XiMat	blood
43	chr1:175904000-175908600	Weak transcription	Primary hematopoietic stem cells	blood
44	chr1:175904200-175908600	Weak transcription	Primary B cells from cord blood	blood
45	chr1:175904200-175908600	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr1:175904200-175909000	Weak transcription	Colon Smooth Muscle	Colon
47	chr1:175904200-175956200	Weak transcription	Psoas Muscle	Psoas
48	chr1:175904400-175908400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr1:175904400-175911800	Strong transcription	Primary T cells from cord blood	blood
50	chr1:175904600-175908800	Weak transcription	Rectal Mucosa Donor 31	rectum

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