Variant report

Variant	rs235877
Chromosome Location	chr1:171614305-171614306
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: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs171001	0.88[CEU][hapmap];0.92[CHB][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs171002	1.00[CEU][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs182907	1.00[CEU][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs183532	0.83[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2032555	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs235861	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs235867	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs235868	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs235869	0.83[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs235870	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs235871	0.91[ASN][1000 genomes]
rs235873	0.91[ASN][1000 genomes]
rs235874	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs235876	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	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs235881	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs235882	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs235913	0.86[YRI][hapmap]
rs483849	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs603490	0.86[ASN][1000 genomes]
rs603930	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs604864	0.83[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs6425364	1.00[CEU][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs86857	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[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:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171605800-171614400	Weak transcription	Aorta	Aorta
2	chr1:171611000-171614600	Enhancers	Primary neutrophils fromperipheralblood	blood
3	chr1:171611200-171614400	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr1:171611400-171614400	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr1:171611400-171614400	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr1:171611400-171614400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr1:171611400-171615800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr1:171612200-171615000	Enhancers	Fetal Brain Male	brain
9	chr1:171612400-171614400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr1:171612800-171614400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr1:171613000-171616200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr1:171613400-171614400	Enhancers	Adipose Nuclei	Adipose
13	chr1:171613600-171615600	Enhancers	Liver	Liver
14	chr1:171613800-171614400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
15	chr1:171613800-171614600	Flanking Active TSS	Fetal Lung	lung
16	chr1:171613800-171615400	Enhancers	Fetal Stomach	stomach
17	chr1:171614000-171614400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr1:171614000-171614400	Enhancers	Primary monocytes fromperipheralblood	blood
19	chr1:171614000-171614400	Enhancers	Primary T cells fromperipheralblood	blood
20	chr1:171614000-171614400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
21	chr1:171614000-171614400	Active TSS	Colonic Mucosa	Colon
22	chr1:171614000-171614400	Enhancers	Skeletal Muscle Male	skeletal muscle
23	chr1:171614000-171614400	Active TSS	Stomach Smooth Muscle	stomach
24	chr1:171614000-171614400	Enhancers	GM12878-XiMat	blood
25	chr1:171614000-171614600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr1:171614000-171614600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr1:171614000-171614600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr1:171614000-171614600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr1:171614000-171614600	Enhancers	Primary T helper naive cells from peripheral blood	blood
30	chr1:171614000-171614600	Flanking Active TSS	Brain Cingulate Gyrus	brain
31	chr1:171614000-171614600	Enhancers	Fetal Intestine Small	intestine
32	chr1:171614000-171614600	Active TSS	Fetal Kidney	kidney
33	chr1:171614000-171614600	Enhancers	Gastric	stomach
34	chr1:171614000-171614600	Enhancers	Pancreas	Pancrea
35	chr1:171614000-171614600	Genic enhancers	Right Atrium	heart
36	chr1:171614000-171614600	Enhancers	Sigmoid Colon	Sigmoid Colon
37	chr1:171614000-171614600	Enhancers	Spleen	Spleen
38	chr1:171614000-171614600	Enhancers	Dnd41	blood
39	chr1:171614000-171614600	Enhancers	HMEC	breast
40	chr1:171614000-171614600	Flanking Active TSS	K562	blood
41	chr1:171614000-171614600	Enhancers	NH-A	brain
42	chr1:171614000-171614600	Flanking Active TSS	NHDF-Ad	bronchial
43	chr1:171614000-171615000	Enhancers	Brain Hippocampus Middle	brain
44	chr1:171614000-171615000	Enhancers	Brain Substantia Nigra	brain
45	chr1:171614000-171615200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr1:171614000-171615200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr1:171614000-171615200	Enhancers	Fetal Brain Female	brain
48	chr1:171614000-171615400	Enhancers	Brain Angular Gyrus	brain
49	chr1:171614000-171615400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
50	chr1:171614000-171615400	Enhancers	Fetal Muscle Leg	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links