Variant report

Variant	rs3176657
Chromosome Location	chr9:100453910-100453911
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	chr9:100453377..100456368-chr9:100458057..100460182,5	MCF-7	breast:
2	chr9:100448159..100450347-chr9:100451447..100454152,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000136936	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs16923033	0.92[AFR][1000 genomes]
rs16923112	0.83[AFR][1000 genomes]
rs1813875	0.92[AFR][1000 genomes]
rs2297155	0.83[AFR][1000 genomes]
rs2297156	0.83[AFR][1000 genomes]
rs2297158	0.83[AFR][1000 genomes]
rs2297159	0.83[AFR][1000 genomes]
rs2297160	0.83[AFR][1000 genomes]
rs2401635	0.83[AFR][1000 genomes]
rs3176623	0.83[AFR][1000 genomes]
rs3176624	0.83[AFR][1000 genomes]
rs3176626	0.83[AFR][1000 genomes]
rs3176628	0.83[AFR][1000 genomes]
rs3176629	0.83[AFR][1000 genomes]
rs3176635	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3176637	0.83[AFR][1000 genomes]
rs3176638	0.83[AFR][1000 genomes]
rs3176644	0.83[AFR][1000 genomes]
rs3176651	0.83[AFR][1000 genomes]
rs3176659	0.83[AFR][1000 genomes]
rs3176668	0.82[AFR][1000 genomes]
rs3176669	0.83[AFR][1000 genomes]
rs3176670	0.83[AFR][1000 genomes]
rs3176675	0.83[AFR][1000 genomes]
rs3176682	0.83[AFR][1000 genomes]
rs3176685	0.83[AFR][1000 genomes]
rs3176687	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3176688	0.80[AFR][1000 genomes]
rs3176694	0.83[AFR][1000 genomes]
rs3176706	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3176708	0.83[AFR][1000 genomes]
rs3176711	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3176712	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3176714	0.83[AFR][1000 genomes]
rs3176720	0.83[AFR][1000 genomes]
rs3176723	0.83[AFR][1000 genomes]
rs3176724	0.83[AFR][1000 genomes]
rs3176726	0.83[AFR][1000 genomes]
rs3176735	0.83[AFR][1000 genomes]
rs3176736	0.83[AFR][1000 genomes]
rs3176740	0.83[AFR][1000 genomes]
rs3176744	0.82[AFR][1000 genomes]
rs3176746	0.83[AFR][1000 genomes]
rs3176747	0.83[AFR][1000 genomes]
rs56052819	0.83[AFR][1000 genomes]
rs56200116	0.82[AFR][1000 genomes]
rs57598118	0.83[AFR][1000 genomes]
rs59354722	0.82[AFR][1000 genomes]
rs59775587	0.83[AFR][1000 genomes]
rs60463150	0.83[AFR][1000 genomes]
rs60821994	0.83[AFR][1000 genomes]
rs61208411	0.83[AFR][1000 genomes]
rs61440789	0.82[AFR][1000 genomes]
rs61739366	0.87[AFR][1000 genomes]
rs6478305	0.87[AFR][1000 genomes]
rs7021377	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7045160	0.83[AFR][1000 genomes]
rs73498323	0.89[AFR][1000 genomes]
rs73498329	0.91[AFR][1000 genomes]
rs73498359	0.92[AFR][1000 genomes]
rs73498365	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73498377	0.83[AFR][1000 genomes]
rs73498380	0.83[AFR][1000 genomes]
rs73498381	0.83[AFR][1000 genomes]
rs73500307	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73500321	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73500325	0.83[AFR][1000 genomes]
rs73500328	0.83[AFR][1000 genomes]
rs73500392	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73500393	0.83[AFR][1000 genomes]
rs73500395	0.83[AFR][1000 genomes]
rs73500396	0.83[AFR][1000 genomes]
rs73500397	0.83[AFR][1000 genomes]
rs73500398	0.83[AFR][1000 genomes]
rs73500400	0.83[AFR][1000 genomes]
rs73502208	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs73502210	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs73551090	0.87[AFR][1000 genomes]
rs73554650	0.88[AFR][1000 genomes]
rs7850986	0.83[AFR][1000 genomes]
rs7857174	0.88[AFR][1000 genomes]
rs7859979	0.88[AFR][1000 genomes]
rs7862356	0.83[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893610	chr9:100324086-100496160	Active TSS Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:100401200-100456000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
2	chr9:100402400-100455600	Strong transcription	Dnd41	blood
3	chr9:100402600-100456000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr9:100402600-100456200	Strong transcription	Primary B cells from peripheral blood	blood
5	chr9:100402800-100454200	Strong transcription	Fetal Thymus	thymus
6	chr9:100402800-100456000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr9:100403000-100454400	Strong transcription	Placenta	Placenta
8	chr9:100403000-100454600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
9	chr9:100403200-100454400	Strong transcription	Rectal Mucosa Donor 31	rectum
10	chr9:100403200-100455000	Strong transcription	Primary T cells fromperipheralblood	blood
11	chr9:100404800-100455400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr9:100410200-100454000	Strong transcription	Fetal Muscle Trunk	muscle
13	chr9:100412600-100454200	Strong transcription	Duodenum Smooth Muscle	Duodenum
14	chr9:100423000-100456000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr9:100429200-100455000	Strong transcription	Primary T helper cells PMA-I stimulated	--
16	chr9:100429200-100455600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr9:100429600-100454000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr9:100429600-100455400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr9:100429600-100455800	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr9:100429800-100456000	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr9:100434400-100455600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr9:100436600-100454600	Strong transcription	Adipose Nuclei	Adipose
23	chr9:100437400-100456000	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr9:100437600-100455800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr9:100437600-100458400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr9:100438000-100458400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr9:100438400-100457200	Weak transcription	Psoas Muscle	Psoas
28	chr9:100438400-100457400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr9:100438600-100457800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr9:100439000-100458800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr9:100439800-100454400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr9:100440000-100454400	Strong transcription	Fetal Muscle Leg	muscle
33	chr9:100442000-100454000	Strong transcription	Primary neutrophils fromperipheralblood	blood
34	chr9:100442000-100454000	Strong transcription	Colon Smooth Muscle	Colon
35	chr9:100442000-100455200	Strong transcription	Primary T helper cells fromperipheralblood	blood
36	chr9:100442200-100454000	Strong transcription	Sigmoid Colon	Sigmoid Colon
37	chr9:100442200-100454200	Strong transcription	Brain Germinal Matrix	brain
38	chr9:100445000-100455000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr9:100446400-100454400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr9:100446800-100456800	Weak transcription	Small Intestine	intestine
41	chr9:100446800-100457600	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr9:100446800-100457800	Weak transcription	Aorta	Aorta
43	chr9:100447000-100457800	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr9:100447200-100456400	Weak transcription	K562	blood
45	chr9:100447200-100457200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
46	chr9:100447200-100457400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr9:100447200-100458400	Weak transcription	Colonic Mucosa	Colon
48	chr9:100448600-100454000	Strong transcription	Thymus	Thymus
49	chr9:100448600-100454600	Strong transcription	Fetal Stomach	stomach
50	chr9:100448600-100455800	Strong transcription	Fetal Brain Female	brain

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