Variant report

Variant	rs247242
Chromosome Location	chr5:61726547-61726548
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:61696731..61700669-chr5:61725889..61729809,4	MCF-7	breast:
2	chr5:61721758..61724717-chr5:61725475..61727372,2	K562	blood:
3	chr5:61719601..61722587-chr5:61724504..61726966,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000086200	Chromatin interaction
ENSG00000086189	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10058598	0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10069988	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs101091	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12517326	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1301064	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1301065	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13361219	0.84[ASN][1000 genomes]
rs152186	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs152204	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs152205	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs152210	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16890800	0.82[ASN][1000 genomes]
rs247225	0.94[ASN][1000 genomes]
rs247227	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs247231	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs247232	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs247237	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs247241	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs247243	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs247250	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs247251	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs247254	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs247259	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs247262	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs247264	0.86[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs247266	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs247479	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs26635	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs26639	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs26642	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs27089	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs27448	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs27449	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs27931	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs35119	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35348760	0.84[ASN][1000 genomes]
rs4145851	0.82[ASN][1000 genomes]
rs767159	0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs784916	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs784918	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9632387	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024090	chr5:61258759-61921150	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	esv2759345	chr5:61403138-61748912	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv1020255	chr5:61451792-62031365	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv1027539	chr5:61457762-62000008	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv1033578	chr5:61606610-61911153	Active TSS Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	nsv1025145	chr5:61624735-61824265	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	nsv1029708	chr5:61625813-61877628	Bivalent/Poised TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
8	nsv881728	chr5:61630879-61857577	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
9	esv2757117	chr5:61649403-61748912	Weak transcription Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
10	nsv598348	chr5:61650843-61895124	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
11	esv35035	chr5:61657943-61792243	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
12	nsv881729	chr5:61719506-61857577	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:61709200-61770800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr5:61709400-61727400	Weak transcription	Placenta	Placenta
3	chr5:61709400-61727400	Weak transcription	Pancreas	Pancrea
4	chr5:61709400-61763400	Weak transcription	Aorta	Aorta
5	chr5:61709600-61728000	Weak transcription	Gastric	stomach
6	chr5:61709600-61738800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr5:61709600-61738800	Weak transcription	Fetal Muscle Trunk	muscle
8	chr5:61709600-61739800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr5:61709600-61744000	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr5:61709800-61727400	Weak transcription	HSMM	muscle
11	chr5:61709800-61728000	Weak transcription	Fetal Lung	lung
12	chr5:61709800-61728000	Weak transcription	Right Ventricle	heart
13	chr5:61709800-61728000	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr5:61709800-61728200	Weak transcription	Brain Hippocampus Middle	brain
15	chr5:61709800-61738800	Weak transcription	Fetal Kidney	kidney
16	chr5:61709800-61743800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr5:61709800-61746000	Weak transcription	Primary hematopoietic stem cells	blood
18	chr5:61709800-61746600	Weak transcription	Fetal Thymus	thymus
19	chr5:61709800-61769000	Weak transcription	NH-A	brain
20	chr5:61709800-61809200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr5:61710000-61727000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr5:61710000-61727200	Weak transcription	Fetal Muscle Leg	muscle
23	chr5:61710000-61727600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr5:61710000-61729000	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr5:61710000-61734200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr5:61710000-61734200	Weak transcription	Fetal Intestine Small	intestine
27	chr5:61710000-61737400	Weak transcription	Fetal Intestine Large	intestine
28	chr5:61710000-61739000	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr5:61710000-61746000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr5:61710200-61728000	Weak transcription	Stomach Smooth Muscle	stomach
31	chr5:61710200-61733400	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr5:61710200-61738800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr5:61710200-61746000	Weak transcription	Primary B cells from cord blood	blood
34	chr5:61710400-61733600	Weak transcription	Primary T helper cells fromperipheralblood	blood
35	chr5:61710400-61739000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr5:61710400-61746000	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr5:61710600-61738800	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr5:61710600-61739000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr5:61710600-61739200	Weak transcription	HMEC	breast
40	chr5:61710600-61739200	Weak transcription	NHEK	skin
41	chr5:61710600-61744000	Weak transcription	Primary T helper cells PMA-I stimulated	--
42	chr5:61710600-61746000	Weak transcription	A549	lung
43	chr5:61710800-61727200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr5:61710800-61727400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr5:61710800-61727800	Weak transcription	Liver	Liver
46	chr5:61710800-61728000	Weak transcription	Fetal Brain Female	brain
47	chr5:61710800-61739000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr5:61710800-61745400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
49	chr5:61710800-61746000	Weak transcription	HepG2	liver
50	chr5:61711000-61733400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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