Variant report

Variant	rs1781740
Chromosome Location	chr6:38614198-38614199
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:38613336..38615635-chr6:38618422..38620707,2	K562	blood:
2	chr6:38605341..38608804-chr6:38614063..38616688,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-DNAH8-8	chr6:38607926-38617146	NONHSAT112318

Variant related genes	Relation type
ENSG00000183826	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs12154188	0.84[CEU][hapmap]
rs1699013	0.85[CEU][hapmap]
rs1699014	0.95[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs1699015	0.86[ASW][hapmap];0.92[CEU][hapmap];0.80[TSI][hapmap];0.82[EUR][1000 genomes]
rs1699018	0.93[ASW][hapmap];0.92[CEU][hapmap];0.80[TSI][hapmap];0.82[YRI][hapmap];0.82[EUR][1000 genomes]
rs1699020	0.85[CEU][hapmap]
rs17543429	0.83[CEU][hapmap];1.00[JPT][hapmap]
rs17614684	1.00[JPT][hapmap]
rs1781741	0.85[CEU][hapmap]
rs1781742	0.93[ASW][hapmap];0.96[CEU][hapmap];0.85[CHB][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.96[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs2748156	0.85[CEU][hapmap];0.82[TSI][hapmap]
rs2748166	0.85[CEU][hapmap]
rs2748168	0.85[CEU][hapmap]
rs2748173	0.85[CEU][hapmap];0.88[TSI][hapmap]
rs2814887	0.88[CEU][hapmap]
rs2814890	0.85[CEU][hapmap];0.88[TSI][hapmap]
rs2814893	0.85[CEU][hapmap]
rs6458060	0.92[CEU][hapmap];0.80[EUR][1000 genomes]
rs6924443	0.85[CEU][hapmap];0.82[TSI][hapmap]
rs6927145	0.86[CEU][hapmap]
rs7752239	0.84[CEU][hapmap]
rs7761154	0.85[CEU][hapmap]
rs7769186	0.85[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021991	chr6:37893949-38738720	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv885817	chr6:38036420-39019503	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	esv2758049	chr6:38588969-38711085	Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	esv2759421	chr6:38588969-38711085	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	nsv427754	chr6:38588969-38711085	Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
6	nsv428144	chr6:38588969-38711085	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1781740	TAF11	cis	cerebellum	SCAN
rs1781740	MDFI	cis	cerebellum	SCAN
rs1781740	GLO1	cis	cerebellum	SCAN
rs1781740	ANKS1A	cis	cerebellum	SCAN
rs1781740	GLO1	cis	parietal	SCAN

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:38608800-38614200	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr6:38608800-38618000	Weak transcription	Aorta	Aorta
3	chr6:38609000-38617200	Weak transcription	Small Intestine	intestine
4	chr6:38609000-38618800	Weak transcription	Primary hematopoietic stem cells	blood
5	chr6:38609000-38623600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr6:38609000-38624600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr6:38609000-38625600	Weak transcription	Fetal Stomach	stomach
8	chr6:38609000-38628200	Weak transcription	Rectal Smooth Muscle	rectum
9	chr6:38609000-38634200	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr6:38609000-38641200	Weak transcription	Pancreas	Pancrea
11	chr6:38609000-38641200	Weak transcription	Spleen	Spleen
12	chr6:38609000-38642000	Weak transcription	Primary T cells from cord blood	blood
13	chr6:38609000-38645200	Weak transcription	Fetal Intestine Small	intestine
14	chr6:38609000-38645600	Weak transcription	Left Ventricle	heart
15	chr6:38609200-38615800	Weak transcription	Primary B cells from peripheral blood	blood
16	chr6:38609200-38621000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr6:38609200-38641200	Weak transcription	Primary B cells from cord blood	blood
18	chr6:38609200-38642400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr6:38609200-38643400	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr6:38609400-38614200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr6:38609400-38642200	Weak transcription	Stomach Smooth Muscle	stomach
22	chr6:38609600-38642800	Weak transcription	Brain Cingulate Gyrus	brain
23	chr6:38609800-38618000	Weak transcription	Right Atrium	heart
24	chr6:38609800-38624400	Weak transcription	Psoas Muscle	Psoas
25	chr6:38609800-38643000	Weak transcription	Colon Smooth Muscle	Colon
26	chr6:38611800-38615200	Enhancers	Fetal Brain Female	brain
27	chr6:38612800-38615200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr6:38612800-38623400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr6:38612800-38641600	Weak transcription	Adipose Nuclei	Adipose
30	chr6:38612800-38648400	Weak transcription	Brain Anterior Caudate	brain
31	chr6:38612800-38652800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr6:38613000-38642400	Weak transcription	Fetal Lung	lung
33	chr6:38613200-38615200	Enhancers	Fetal Brain Male	brain
34	chr6:38613400-38641200	Weak transcription	Liver	Liver
35	chr6:38613600-38614400	Enhancers	HUES64 Cell Line	embryonic stem cell
36	chr6:38613600-38614600	Enhancers	HUES6 Cell Line	embryonic stem cell
37	chr6:38613600-38614600	Enhancers	iPS-15b Cell Line	embryonic stem cell
38	chr6:38613600-38614800	Enhancers	ES-I3 Cell Line	embryonic stem cell
39	chr6:38613600-38614800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr6:38613800-38614400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr6:38613800-38614400	Enhancers	NHDF-Ad	bronchial
42	chr6:38613800-38614400	Enhancers	NHEK	skin
43	chr6:38613800-38614600	Enhancers	HUES48 Cell Line	embryonic stem cell
44	chr6:38613800-38614800	Enhancers	Brain Angular Gyrus	brain
45	chr6:38613800-38615200	Enhancers	Ovary	ovary
46	chr6:38613800-38615400	Weak transcription	Skeletal Muscle Male	skeletal muscle

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