Variant report

Variant	rs235876
Chromosome Location	chr1:171614114-171614115
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:171613978..171614654-chr1:171684466..171685390,3	MCF-7	breast:
2	chr1:171613874..171614671-chr1:171684707..171685402,3	MCF-7	breast:
3	chr1:171613993..171614607-chr1:171624519..171625315,2	MCF-7	breast:
4	chr1:171613767..171614432-chr1:171685019..171685719,2	K562	blood:
5	chr1:171613352..171616352-chr1:171748530..171751285,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000010165	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs171001	0.88[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs171002	1.00[CEU][hapmap];0.81[JPT][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs182907	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs183532	0.92[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2032555	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.96[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs235861	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs235867	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs235868	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs235869	0.92[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs235870	0.92[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs235871	0.93[ASN][1000 genomes]
rs235873	0.93[ASN][1000 genomes]
rs235874	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs235877	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs235878	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs235881	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs235882	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs483849	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs603490	0.88[ASN][1000 genomes]
rs603930	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.96[GIH][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs604864	0.92[CHB][hapmap];0.80[CHD][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs6425364	1.00[CEU][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs86857	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[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	esv14617	chr1:171016086-171726961	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer 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	52 gene(s)	inside rSNPs	diseases
2	esv3512995	chr1:171329123-171994470	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	esv3512997	chr1:171329123-171994470	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	esv12447	chr1:171556291-171726822	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs235876	DNM3	cis	cerebellum	SCAN

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171605800-171614400	Weak transcription	Aorta	Aorta
2	chr1:171610800-171614200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr1:171611000-171614600	Enhancers	Primary neutrophils fromperipheralblood	blood
4	chr1:171611200-171614400	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr1:171611400-171614200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr1:171611400-171614400	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr1:171611400-171614400	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr1:171611400-171614400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr1:171611400-171615800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr1:171611600-171614200	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr1:171611600-171614200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr1:171612200-171615000	Enhancers	Fetal Brain Male	brain
13	chr1:171612400-171614400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr1:171612800-171614400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr1:171613000-171616200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr1:171613400-171614400	Enhancers	Adipose Nuclei	Adipose
17	chr1:171613600-171615600	Enhancers	Liver	Liver
18	chr1:171613800-171614200	Enhancers	Duodenum Mucosa	Duodenum
19	chr1:171613800-171614400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
20	chr1:171613800-171614600	Flanking Active TSS	Fetal Lung	lung
21	chr1:171613800-171615400	Enhancers	Fetal Stomach	stomach
22	chr1:171614000-171614200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
23	chr1:171614000-171614200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr1:171614000-171614200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr1:171614000-171614200	Enhancers	Colon Smooth Muscle	Colon
26	chr1:171614000-171614200	Enhancers	Rectal Mucosa Donor 29	rectum
27	chr1:171614000-171614200	Enhancers	Rectal Smooth Muscle	rectum
28	chr1:171614000-171614200	Enhancers	Thymus	Thymus
29	chr1:171614000-171614200	Flanking Active TSS	Hela-S3	cervix
30	chr1:171614000-171614200	Flanking Active TSS	HepG2	liver
31	chr1:171614000-171614400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr1:171614000-171614400	Enhancers	Primary monocytes fromperipheralblood	blood
33	chr1:171614000-171614400	Enhancers	Primary T cells fromperipheralblood	blood
34	chr1:171614000-171614400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
35	chr1:171614000-171614400	Active TSS	Colonic Mucosa	Colon
36	chr1:171614000-171614400	Enhancers	Skeletal Muscle Male	skeletal muscle
37	chr1:171614000-171614400	Active TSS	Stomach Smooth Muscle	stomach
38	chr1:171614000-171614400	Enhancers	GM12878-XiMat	blood
39	chr1:171614000-171614600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr1:171614000-171614600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr1:171614000-171614600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr1:171614000-171614600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr1:171614000-171614600	Enhancers	Primary T helper naive cells from peripheral blood	blood
44	chr1:171614000-171614600	Flanking Active TSS	Brain Cingulate Gyrus	brain
45	chr1:171614000-171614600	Enhancers	Fetal Intestine Small	intestine
46	chr1:171614000-171614600	Active TSS	Fetal Kidney	kidney
47	chr1:171614000-171614600	Enhancers	Gastric	stomach
48	chr1:171614000-171614600	Enhancers	Pancreas	Pancrea
49	chr1:171614000-171614600	Genic enhancers	Right Atrium	heart
50	chr1:171614000-171614600	Enhancers	Sigmoid Colon	Sigmoid Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links