Variant report

Variant	rs1781741
Chromosome Location	chr6:38612520-38612521
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:38612414-38612591	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr6:38612470-38612881	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:38607481..38610095-chr6:38610442..38613848,3	MCF-7	breast:
2	chr6:38610308..38612975-chr6:38669133..38671766,2	K562	blood:

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

Variant related genes	Relation type
BTBD9	TF binding region
ENSG00000124767	Chromatin interaction
ENSG00000183826	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs12525759	1.00[JPT][hapmap]
rs16890826	0.89[JPT][hapmap]
rs16890840	0.94[JPT][hapmap]
rs1699006	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1699013	1.00[CEU][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1699015	0.85[CEU][hapmap]
rs1699018	0.85[CEU][hapmap]
rs1699020	1.00[CEU][hapmap];0.84[JPT][hapmap];0.81[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1739622	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1739625	0.89[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1781739	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1781740	0.85[CEU][hapmap]
rs1781742	0.88[CEU][hapmap]
rs2748166	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2748168	1.00[CEU][hapmap];0.89[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2748169	0.89[JPT][hapmap]
rs2814891	0.89[JPT][hapmap]
rs2814893	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6458060	0.82[CEU][hapmap]
rs7769186	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]

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

No data

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:38608800-38613600	Weak transcription	HUES64 Cell Line	embryonic stem cell
2	chr6:38608800-38614200	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr6:38608800-38618000	Weak transcription	Aorta	Aorta
4	chr6:38609000-38612800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr6:38609000-38613200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr6:38609000-38613600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr6:38609000-38613600	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr6:38609000-38613600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr6:38609000-38617200	Weak transcription	Small Intestine	intestine
10	chr6:38609000-38618800	Weak transcription	Primary hematopoietic stem cells	blood
11	chr6:38609000-38623600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr6:38609000-38624600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr6:38609000-38625600	Weak transcription	Fetal Stomach	stomach
14	chr6:38609000-38628200	Weak transcription	Rectal Smooth Muscle	rectum
15	chr6:38609000-38634200	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr6:38609000-38641200	Weak transcription	Pancreas	Pancrea
17	chr6:38609000-38641200	Weak transcription	Spleen	Spleen
18	chr6:38609000-38642000	Weak transcription	Primary T cells from cord blood	blood
19	chr6:38609000-38645200	Weak transcription	Fetal Intestine Small	intestine
20	chr6:38609000-38645600	Weak transcription	Left Ventricle	heart
21	chr6:38609200-38612600	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr6:38609200-38613800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr6:38609200-38613800	Weak transcription	NHEK	skin
24	chr6:38609200-38615800	Weak transcription	Primary B cells from peripheral blood	blood
25	chr6:38609200-38621000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr6:38609200-38641200	Weak transcription	Primary B cells from cord blood	blood
27	chr6:38609200-38642400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr6:38609200-38643400	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr6:38609400-38613800	Weak transcription	NHDF-Ad	bronchial
30	chr6:38609400-38614200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr6:38609400-38642200	Weak transcription	Stomach Smooth Muscle	stomach
32	chr6:38609600-38642800	Weak transcription	Brain Cingulate Gyrus	brain
33	chr6:38609800-38613800	Weak transcription	Ovary	ovary
34	chr6:38609800-38618000	Weak transcription	Right Atrium	heart
35	chr6:38609800-38624400	Weak transcription	Psoas Muscle	Psoas
36	chr6:38609800-38643000	Weak transcription	Colon Smooth Muscle	Colon
37	chr6:38611800-38612800	Enhancers	Fetal Brain Male	brain
38	chr6:38611800-38613600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr6:38611800-38615200	Enhancers	Fetal Brain Female	brain
40	chr6:38612200-38612800	Enhancers	Adipose Nuclei	Adipose
41	chr6:38612200-38612800	Enhancers	Brain Angular Gyrus	brain
42	chr6:38612200-38612800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
43	chr6:38612200-38613400	Enhancers	Liver	Liver
44	chr6:38612400-38612800	Enhancers	Breast Myoepithelial Primary Cells	Breast
45	chr6:38612400-38612800	Enhancers	Brain Anterior Caudate	brain
46	chr6:38612400-38612800	Enhancers	GM12878-XiMat	blood
47	chr6:38612400-38613000	Enhancers	Fetal Lung	lung
48	chr6:38612400-38613800	Enhancers	Skeletal Muscle Male	skeletal muscle

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