Variant report

Variant	rs235874
Chromosome Location	chr1:171613516-171613517
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	chr1:171611915..171613655-chr1:171683755..171685490,3	MCF-7	breast:
2	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: 0)

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

rs_ID	r²[population]
rs171001	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs171002	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs182907	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs183532	0.94[ASN][1000 genomes]
rs2032555	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs235861	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs235867	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs235868	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs235869	0.95[ASN][1000 genomes]
rs235870	0.95[ASN][1000 genomes]
rs235871	0.95[ASN][1000 genomes]
rs235873	0.95[ASN][1000 genomes]
rs235876	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs235877	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs235878	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs235881	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs235882	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs483849	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs603490	0.90[ASN][1000 genomes]
rs603930	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs604864	0.90[ASN][1000 genomes]
rs6425364	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs86857	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[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

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171605800-171614400	Weak transcription	Aorta	Aorta
2	chr1:171607800-171614000	Weak transcription	HepG2	liver
3	chr1:171610000-171614000	Weak transcription	Spleen	Spleen
4	chr1:171610800-171614000	Weak transcription	Ovary	ovary
5	chr1:171610800-171614200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr1:171611000-171614000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr1:171611000-171614600	Enhancers	Primary neutrophils fromperipheralblood	blood
8	chr1:171611200-171613800	Weak transcription	Stomach Smooth Muscle	stomach
9	chr1:171611200-171614000	Weak transcription	Right Atrium	heart
10	chr1:171611200-171614400	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr1:171611400-171614200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr1:171611400-171614400	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr1:171611400-171614400	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr1:171611400-171614400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr1:171611400-171615800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr1:171611600-171613600	Weak transcription	Liver	Liver
17	chr1:171611600-171614000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr1:171611600-171614200	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr1:171611600-171614200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr1:171612200-171615000	Enhancers	Fetal Brain Male	brain
21	chr1:171612400-171614400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr1:171612800-171614000	Weak transcription	Fetal Brain Female	brain
23	chr1:171612800-171614400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr1:171613000-171616200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr1:171613400-171614400	Enhancers	Adipose Nuclei	Adipose

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links