Variant report

Variant	rs7872648
Chromosome Location	chr9:97891309-97891310
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:97678927..97686235-chr9:97889117..97896057,11	MCF-7	breast:
2	chr9:97315606..97318346-chr9:97888439..97891401,2	MCF-7	breast:
3	chr9:97544700..97548107-chr9:97891004..97896251,5	MCF-7	breast:
4	chr9:97765404..97770153-chr9:97890107..97893665,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000231806	Chromatin interaction
ENSG00000148120	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10115247	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10739992	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10739993	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10761377	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10821451	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10821453	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10821454	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10821455	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10993490	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13295862	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17686583	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1979022	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2166402	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2282216	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2297596	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2297597	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2404457	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3277	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34045846	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34532504	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3737142	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3780561	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3780562	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3780564	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3780567	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3780568	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3824486	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3844341	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3852402	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4647382	0.82[EUR][1000 genomes]
rs4647443	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4647459	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4647462	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4647475	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4647528	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4647529	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4647534	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4647554	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4647558	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4744446	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4744451	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6479601	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7019043	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7023007	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7027204	0.82[EUR][1000 genomes]
rs7034538	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7850958	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7854570	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7874310	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs879492	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs881791	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs963774	0.88[AMR][1000 genomes];0.92[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	nsv933919	chr9:97619512-97919344	Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	293 gene(s)	inside rSNPs	diseases
2	nsv1038523	chr9:97797032-97923774	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	274 gene(s)	inside rSNPs	diseases
3	nsv540175	chr9:97797032-97923774	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	274 gene(s)	inside rSNPs	diseases
4	nsv831656	chr9:97831551-97989980	Weak transcription Strong transcription Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	274 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97844000-97898400	Weak transcription	Primary T helper cells fromperipheralblood	blood
2	chr9:97875400-97895400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr9:97875400-97900400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr9:97875600-97900000	Weak transcription	Spleen	Spleen
5	chr9:97875600-97906000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr9:97875800-97892200	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr9:97877000-97892000	Weak transcription	Gastric	stomach
8	chr9:97877000-97896400	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr9:97884600-97892000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr9:97887200-97891600	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr9:97887200-97891600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr9:97887400-97916400	Weak transcription	Thymus	Thymus
13	chr9:97887800-97891400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr9:97888000-97900000	Weak transcription	Primary T cells from cord blood	blood
15	chr9:97888600-97891600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr9:97890000-97891600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr9:97890000-97891600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr9:97890000-97891600	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr9:97890000-97891800	Weak transcription	Liver	Liver
20	chr9:97890000-97891800	Weak transcription	Brain Substantia Nigra	brain
21	chr9:97890000-97891800	Weak transcription	Fetal Intestine Large	intestine
22	chr9:97890000-97891800	Weak transcription	Fetal Intestine Small	intestine
23	chr9:97890000-97892000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr9:97890000-97892000	Weak transcription	Duodenum Mucosa	Duodenum
25	chr9:97890000-97892000	Weak transcription	Fetal Lung	lung
26	chr9:97890000-97892000	Weak transcription	Lung	lung
27	chr9:97890000-97892000	Weak transcription	Pancreas	Pancrea
28	chr9:97890000-97892000	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr9:97890000-97892600	Enhancers	ES-I3 Cell Line	embryonic stem cell
30	chr9:97890000-97892800	Enhancers	iPS-18 Cell Line	embryonic stem cell
31	chr9:97890000-97893400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr9:97890000-97893400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr9:97890000-97893400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr9:97890000-97893400	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr9:97890000-97893400	Weak transcription	Adipose Nuclei	Adipose
36	chr9:97890000-97893400	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr9:97890000-97893400	Weak transcription	Ovary	ovary
38	chr9:97890000-97893400	Weak transcription	Psoas Muscle	Psoas
39	chr9:97890000-97893600	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr9:97890000-97894600	Weak transcription	Fetal Muscle Leg	muscle
41	chr9:97890000-97894600	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr9:97890000-97895200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr9:97890000-97898600	Weak transcription	Left Ventricle	heart
44	chr9:97890000-97898600	Weak transcription	Right Atrium	heart
45	chr9:97890000-97900000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr9:97890000-97906600	Weak transcription	Right Ventricle	heart
47	chr9:97890000-97919600	Weak transcription	Hela-S3	cervix
48	chr9:97890000-97928000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr9:97890200-97891400	Weak transcription	H9 Cell Line	embryonic stem cell
50	chr9:97890200-97891600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links