Variant report

Variant	rs55967209
Chromosome Location	chr5:179203264-179203265
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:179201375..179203959-chr5:179207512..179210271,2	MCF-7	breast:
2	chr5:179194709..179196943-chr5:179203139..179205240,2	K562	blood:
3	chr5:179201693..179205348-chr5:179210724..179213200,3	MCF-7	breast:
4	chr5:179194910..179198066-chr5:179199743..179203890,4	K562	blood:
5	chr5:179202322..179204909-chr5:179246443..179248610,2	MCF-7	breast:
6	chr5:179202717..179204646-chr5:179228468..179231220,2	K562	blood:
7	chr5:179190740..179195492-chr5:179198923..179204539,8	MCF-7	breast:

Variant related genes	Relation type
ENSG00000161013	Chromatin interaction
ENSG00000161011	Chromatin interaction
ENSG00000161021	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs2291417	0.91[AMR][1000 genomes]
rs2291418	0.91[AMR][1000 genomes]
rs55800082	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55815501	1.00[EUR][1000 genomes]
rs55915939	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55952102	0.94[EUR][1000 genomes]
rs56093222	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56719864	0.91[AFR][1000 genomes]
rs57463529	0.96[AFR][1000 genomes]
rs58722253	0.96[AFR][1000 genomes]
rs58826518	0.91[AMR][1000 genomes]
rs59108011	0.84[AFR][1000 genomes]
rs59566858	0.96[AFR][1000 genomes]
rs59651103	0.96[AFR][1000 genomes]
rs59721505	0.96[AFR][1000 genomes]
rs59745533	0.96[AFR][1000 genomes]
rs59824837	0.96[AFR][1000 genomes]
rs60485189	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60716268	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60910702	0.87[AFR][1000 genomes]
rs61682673	0.96[AFR][1000 genomes]
rs66465242	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs66685266	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs66686562	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs66995745	0.91[AMR][1000 genomes]
rs67211456	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs67637906	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs67832593	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs67879510	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs67952129	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6865507	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72807319	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72807328	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72807332	1.00[EUR][1000 genomes]
rs72807337	1.00[EUR][1000 genomes]
rs72809763	0.94[EUR][1000 genomes]
rs72809769	0.94[EUR][1000 genomes]
rs72809771	0.94[EUR][1000 genomes]
rs72809773	0.94[EUR][1000 genomes]
rs72809775	1.00[EUR][1000 genomes]
rs72809781	1.00[EUR][1000 genomes]
rs72809782	1.00[EUR][1000 genomes]
rs72809783	1.00[EUR][1000 genomes]
rs72809785	1.00[EUR][1000 genomes]
rs72809787	1.00[EUR][1000 genomes]
rs72809790	1.00[EUR][1000 genomes]
rs72809792	1.00[EUR][1000 genomes]
rs72809794	1.00[EUR][1000 genomes]
rs72809795	1.00[EUR][1000 genomes]
rs72809796	1.00[EUR][1000 genomes]
rs72809798	1.00[EUR][1000 genomes]
rs72809802	1.00[EUR][1000 genomes]
rs73338115	0.88[AFR][1000 genomes]
rs73342167	0.96[AFR][1000 genomes]
rs73347986	0.96[AFR][1000 genomes]
rs73349908	0.96[AFR][1000 genomes]
rs73351620	0.84[AFR][1000 genomes]
rs73351626	0.84[AFR][1000 genomes]
rs73351628	0.84[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949554	chr5:178832325-179309513	Transcr. at gene 5' and 3' Weak transcription Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	312 gene(s)	inside rSNPs	diseases
2	nsv883270	chr5:178951106-179350387	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	312 gene(s)	inside rSNPs	diseases
3	nsv531997	chr5:179107599-179588082	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	339 gene(s)	inside rSNPs	diseases
4	nsv469579	chr5:179184831-179360191	Genic enhancers Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	182 gene(s)	inside rSNPs	diseases
5	nsv883274	chr5:179186397-179310330	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
6	nsv518964	chr5:179193598-179227286	Strong transcription Enhancers Active TSS Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	151 gene(s)	inside rSNPs	diseases
7	nsv883275	chr5:179193598-179267783	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	176 gene(s)	inside rSNPs	diseases
8	nsv883276	chr5:179193598-179310330	Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS 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 miRNA target site	178 gene(s)	inside rSNPs	diseases
9	nsv883277	chr5:179193598-179350387	Genic enhancers Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	182 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179190800-179207600	Strong transcription	Dnd41	blood
2	chr5:179191200-179210400	Strong transcription	Thymus	Thymus
3	chr5:179192000-179207800	Strong transcription	Fetal Thymus	thymus
4	chr5:179192200-179206200	Strong transcription	HUES48 Cell Line	embryonic stem cell
5	chr5:179192200-179206200	Strong transcription	Primary B cells from peripheral blood	blood
6	chr5:179192200-179206400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr5:179192200-179206400	Strong transcription	HepG2	liver
8	chr5:179192200-179207600	Strong transcription	Fetal Lung	lung
9	chr5:179192200-179207800	Strong transcription	Primary T helper cells fromperipheralblood	blood
10	chr5:179192200-179208000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
11	chr5:179192200-179210400	Strong transcription	Brain Germinal Matrix	brain
12	chr5:179192400-179203600	Strong transcription	H9 Cell Line	embryonic stem cell
13	chr5:179192400-179205400	Strong transcription	Sigmoid Colon	Sigmoid Colon
14	chr5:179192400-179206200	Strong transcription	GM12878-XiMat	blood
15	chr5:179192400-179207600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr5:179192400-179207600	Strong transcription	Rectal Mucosa Donor 31	rectum
17	chr5:179192600-179209800	Strong transcription	Primary T cells from cord blood	blood
18	chr5:179192800-179205200	Strong transcription	Rectal Smooth Muscle	rectum
19	chr5:179192800-179207200	Strong transcription	Fetal Muscle Leg	muscle
20	chr5:179192800-179209800	Strong transcription	Fetal Brain Female	brain
21	chr5:179193000-179210400	Strong transcription	Fetal Stomach	stomach
22	chr5:179193400-179207600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr5:179193400-179207800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr5:179193400-179208000	Strong transcription	Lung	lung
25	chr5:179193600-179203600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr5:179193600-179204600	Strong transcription	Placenta	Placenta
27	chr5:179193600-179206000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr5:179193600-179206800	Strong transcription	Fetal Muscle Trunk	muscle
29	chr5:179193600-179207600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr5:179193600-179207600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr5:179193600-179209600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr5:179193800-179204000	Strong transcription	Left Ventricle	heart
33	chr5:179193800-179204000	Strong transcription	HSMM	muscle
34	chr5:179193800-179206200	Strong transcription	Primary T cells fromperipheralblood	blood
35	chr5:179193800-179206200	Strong transcription	HSMMtube	muscle
36	chr5:179193800-179207000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr5:179193800-179207400	Strong transcription	HUES6 Cell Line	embryonic stem cell
38	chr5:179193800-179207600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr5:179193800-179207800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
40	chr5:179193800-179207800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
41	chr5:179193800-179207800	Strong transcription	Rectal Mucosa Donor 29	rectum
42	chr5:179193800-179208400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr5:179193800-179209400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr5:179193800-179209600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr5:179194200-179203600	Strong transcription	Brain Anterior Caudate	brain
46	chr5:179194200-179207400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr5:179194200-179207600	Strong transcription	HUES64 Cell Line	embryonic stem cell
48	chr5:179194400-179206200	Strong transcription	Primary T helper cells PMA-I stimulated	--
49	chr5:179194400-179207400	Strong transcription	Osteobl	bone
50	chr5:179194400-179207600	Strong transcription	Fetal Intestine Large	intestine

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