Variant report

Variant	rs3734377
Chromosome Location	chr6:149285719-149285720
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZC3H12D-3	chr6:149285697-149285820	ENSG00000227660.1
2	lnc-ZC3H12D-3	chr6:149285697-149285820	NONHSAT115482

Extended variants
information (count: 26 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs12194615	0.94[JPT][hapmap]
rs12197795	0.85[CHB][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs12202149	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12204964	0.88[GIH][hapmap]
rs12207855	0.94[JPT][hapmap]
rs12207913	0.94[JPT][hapmap]
rs1384310	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1564601	0.94[JPT][hapmap]
rs1564602	0.94[JPT][hapmap]
rs2340749	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs3734376	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3734378	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4358650	0.94[JPT][hapmap]
rs6570918	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6932862	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6933251	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9322162	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs9377181	0.88[CEU][hapmap];1.00[JPT][hapmap]
rs9377183	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs9377186	0.94[JPT][hapmap]
rs9390646	0.82[ASN][1000 genomes]
rs9404010	0.84[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1032690	chr6:149206106-149398712	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv1032319	chr6:149271433-149550525	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv538470	chr6:149271433-149550525	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv830842	chr6:149272321-149427340	Enhancers Bivalent Enhancer ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3734377	PCMT1	cis	parietal	SCAN
rs3734377	MTHFD1L	cis	cerebellum	SCAN

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:149256600-149292600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr6:149262000-149289600	Weak transcription	Aorta	Aorta
3	chr6:149269400-149288800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr6:149269400-149291400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr6:149271200-149288600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr6:149274000-149286400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr6:149274000-149288800	Weak transcription	NHEK	skin
8	chr6:149274000-149293800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr6:149274200-149288400	Weak transcription	Rectal Smooth Muscle	rectum
10	chr6:149274200-149288800	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr6:149274400-149290400	Weak transcription	Fetal Kidney	kidney
12	chr6:149274600-149288600	Weak transcription	Colon Smooth Muscle	Colon
13	chr6:149274600-149289000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr6:149276400-149287800	Weak transcription	Fetal Muscle Trunk	muscle
15	chr6:149276400-149308400	Weak transcription	Lung	lung
16	chr6:149277800-149289600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr6:149278000-149310600	Weak transcription	Primary hematopoietic stem cells	blood
18	chr6:149280400-149288400	Weak transcription	Right Atrium	heart
19	chr6:149281000-149286400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr6:149281000-149287600	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr6:149281000-149288200	Weak transcription	Fetal Lung	lung
22	chr6:149281000-149288200	Weak transcription	Fetal Muscle Leg	muscle
23	chr6:149283200-149287800	Weak transcription	Gastric	stomach
24	chr6:149283600-149291200	Weak transcription	Fetal Thymus	thymus
25	chr6:149284000-149285800	Enhancers	ES-I3 Cell Line	embryonic stem cell
26	chr6:149284000-149293400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr6:149284200-149285800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
28	chr6:149284400-149288800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr6:149284400-149288800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr6:149284600-149285800	Enhancers	H9 Cell Line	embryonic stem cell
31	chr6:149284600-149286200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr6:149284600-149293400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr6:149284600-149293600	Weak transcription	Esophagus	oesophagus
34	chr6:149284600-149293600	Weak transcription	Ovary	ovary
35	chr6:149285000-149285800	Strong transcription	Spleen	Spleen
36	chr6:149285000-149286600	Strong transcription	Fetal Stomach	stomach
37	chr6:149285000-149286600	Strong transcription	Stomach Smooth Muscle	stomach
38	chr6:149285000-149288400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr6:149285200-149286400	Genic enhancers	iPS-15b Cell Line	embryonic stem cell
40	chr6:149285200-149286600	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr6:149285200-149287000	Strong transcription	Primary B cells from peripheral blood	blood
42	chr6:149285200-149288200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr6:149285200-149288400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr6:149285200-149288800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr6:149285400-149286400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr6:149285400-149286600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr6:149285400-149286600	Strong transcription	Primary B cells from cord blood	blood
48	chr6:149285400-149288400	Weak transcription	HUES48 Cell Line	embryonic stem cell
49	chr6:149285600-149286200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr6:149285600-149286400	Strong transcription	HUES6 Cell Line	embryonic stem cell

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