Variant report

Variant	rs17161677
Chromosome Location	chr7:98929744-98929745
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:98915839..98918656-chr7:98927635..98930198,2	MCF-7	breast:
2	chr7:98921268..98926325-chr7:98927709..98931236,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000241685	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1002172	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1004387	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs10267346	0.85[ASN][1000 genomes]
rs10272998	0.85[JPT][hapmap]
rs10464604	1.00[EUR][1000 genomes]
rs10953286	0.89[JPT][hapmap]
rs11539770	1.00[EUR][1000 genomes]
rs13230554	1.00[CEU][hapmap]
rs17161652	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17161692	0.88[GIH][hapmap];0.85[JPT][hapmap]
rs17161698	1.00[CEU][hapmap];0.96[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1985453	0.96[GIH][hapmap];0.88[MEX][hapmap];1.00[EUR][1000 genomes]
rs2057906	1.00[CEU][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2074652	1.00[JPT][hapmap]
rs2107705	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2240385	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs2269985	1.00[CEU][hapmap];0.96[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2286162	0.85[JPT][hapmap]
rs2301889	0.83[CHB][hapmap];0.88[GIH][hapmap];0.85[JPT][hapmap];0.80[ASN][1000 genomes]
rs2404322	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28468623	0.80[ASN][1000 genomes]
rs3764815	1.00[CEU][hapmap];0.96[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs3800960	1.00[EUR][1000 genomes]
rs3801288	0.84[JPT][hapmap]
rs45492098	1.00[EUR][1000 genomes]
rs45540134	1.00[EUR][1000 genomes]
rs45622743	1.00[EUR][1000 genomes]
rs58222677	1.00[EUR][1000 genomes]
rs58421977	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58660994	0.80[ASN][1000 genomes]
rs58999322	0.97[ASN][1000 genomes]
rs59986060	1.00[EUR][1000 genomes]
rs61159815	1.00[EUR][1000 genomes]
rs61402640	1.00[EUR][1000 genomes]
rs61543997	1.00[EUR][1000 genomes]
rs73395547	0.80[ASN][1000 genomes]
rs73395557	0.80[ASN][1000 genomes]
rs73709637	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73709641	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs940336	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs9768020	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3433144	chr7:98777878-99060209	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv831068	chr7:98819572-99006481	Weak transcription Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:98924400-98957200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr7:98924600-98929800	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr7:98924600-98930200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
4	chr7:98924600-98971600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr7:98924800-98930000	Enhancers	Stomach Mucosa	stomach
6	chr7:98924800-98930800	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr7:98924800-98930800	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr7:98924800-98930800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr7:98924800-98930800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr7:98924800-98930800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr7:98924800-98931000	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr7:98924800-98931000	Weak transcription	Fetal Kidney	kidney
13	chr7:98924800-98932600	Weak transcription	Aorta	Aorta
14	chr7:98924800-98935600	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr7:98924800-98935600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr7:98924800-98935800	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr7:98924800-98936200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr7:98925000-98931000	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr7:98925200-98930800	Weak transcription	Fetal Muscle Trunk	muscle
20	chr7:98925200-98965200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr7:98925400-98935600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr7:98925600-98930200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr7:98925600-98931000	Weak transcription	Thymus	Thymus
24	chr7:98925600-98931200	Weak transcription	Rectal Smooth Muscle	rectum
25	chr7:98925600-98936200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr7:98925800-98930800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr7:98925800-98930800	Weak transcription	Fetal Muscle Leg	muscle
28	chr7:98925800-98930800	Weak transcription	Stomach Smooth Muscle	stomach
29	chr7:98925800-98931200	Weak transcription	Gastric	stomach
30	chr7:98925800-98933600	Weak transcription	Colonic Mucosa	Colon
31	chr7:98926000-98931000	Weak transcription	Fetal Brain Male	brain
32	chr7:98926200-98930800	Weak transcription	Liver	Liver
33	chr7:98926200-98931200	Weak transcription	Brain Cingulate Gyrus	brain
34	chr7:98926200-98934200	Weak transcription	Spleen	Spleen
35	chr7:98926400-98930600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr7:98926400-98930800	Weak transcription	Adipose Nuclei	Adipose
37	chr7:98926400-98931000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr7:98926400-98931200	Weak transcription	Ovary	ovary
39	chr7:98926400-98933000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr7:98926400-98935600	Weak transcription	Brain Substantia Nigra	brain
41	chr7:98926400-98935800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr7:98926600-98930200	Weak transcription	Fetal Stomach	stomach
43	chr7:98926600-98930800	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr7:98926600-98931200	Weak transcription	Lung	lung
45	chr7:98926600-98932600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr7:98926600-98941600	Weak transcription	Psoas Muscle	Psoas
47	chr7:98927000-98929800	Enhancers	NHLF	lung
48	chr7:98927200-98931000	Weak transcription	Brain Anterior Caudate	brain
49	chr7:98927200-98966800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr7:98927400-98930600	Weak transcription	Primary B cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links