Variant report

Variant	rs250226
Chromosome Location	chr5:50259144-50259145
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:25)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:25 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:50258704..50259393-chr5:50669318..50670012,2	MCF-7	breast:
2	chr5:50258356..50259362-chr5:50643286..50644180,12	MCF-7	breast:
3	chr5:50257889..50259548-chr5:50643207..50644436,8	MCF-7	breast:
4	chr5:50258487..50259203-chr5:50675319..50675828,2	MCF-7	breast:
5	chr22:38002849..38003564-chr5:50258729..50259361,2	MCF-7	breast:
6	chr5:50258776..50259398-chr5:50710432..50711334,2	MCF-7	breast:
7	chr5:50258702..50259774-chr6:37758614..37759901,5	K562	blood:
8	chr22:38130913..38131703-chr5:50258465..50259423,2	MCF-7	breast:
9	chr5:50252384..50255461-chr5:50257528..50260468,3	K562	blood:
10	chr22:38077270..38078209-chr5:50258525..50259341,2	MCF-7	breast:
11	chr5:50258512..50259359-chr5:50571455..50572343,4	MCF-7	breast:
12	chr5:50258609..50259346-chr5:51302896..51303496,3	MCF-7	breast:
13	chr5:50258508..50259166-chr6:37709321..37710259,2	K562	blood:
14	chr22:38077435..38078203-chr5:50258653..50259177,2	MCF-7	breast:
15	chr5:50258420..50259533-chr5:51302832..51303666,4	MCF-7	breast:
16	chr5:50258845..50259374-chr5:51136947..51137885,3	MCF-7	breast:
17	chr5:50258501..50259297-chr5:50674472..50675297,2	MCF-7	breast:
18	chr5:50258485..50259288-chr5:50571370..50571987,2	MCF-7	breast:
19	chr5:50258396..50259294-chr5:50980434..50981087,2	MCF-7	breast:
20	chr5:50258756..50259344-chr5:51256471..51257165,2	MCF-7	breast:
21	chr5:50258415..50259414-chr5:50676162..50677552,5	MCF-7	breast:
22	chr5:50258485..50259404-chr5:51952536..51953715,3	K562	blood:
23	chr5:50258785..50259353-chr5:50711781..50713072,4	MCF-7	breast:
24	chr5:50258548..50259403-chr5:52210902..52211872,2	K562	blood:
25	chr5:50258737..50259290-chr5:51136762..51137436,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000259663	Chromatin interaction
ENSG00000100101	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1354171	0.85[AFR][1000 genomes]
rs1374037	1.00[AMR][1000 genomes]
rs173648	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs185136	1.00[AMR][1000 genomes]
rs192223	0.96[AFR][1000 genomes]
rs1993954	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs250225	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs250227	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs250228	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs250231	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs250232	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs250235	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs250239	0.87[AFR][1000 genomes]
rs250240	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs250241	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs250242	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs250243	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs27276	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs31714	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs583124	0.80[AFR][1000 genomes]
rs583125	0.88[AFR][1000 genomes]
rs589372	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs602484	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs614328	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs630982	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs679678	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034445	chr5:49986171-50492609	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv598116	chr5:50064292-50318550	Active TSS Bivalent/Poised TSS Strong transcription Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv830286	chr5:50165805-50374600	Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:50258600-50261600	Active TSS	Stomach Smooth Muscle	stomach
2	chr5:50258600-50266600	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chr5:50258800-50259200	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr5:50258800-50259200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr5:50258800-50259200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr5:50258800-50259200	Active TSS	Rectal Mucosa Donor 29	rectum
7	chr5:50258800-50259400	Flanking Bivalent TSS/Enh	Primary T cells from cord blood	blood
8	chr5:50258800-50259400	Active TSS	NHDF-Ad	bronchial
9	chr5:50258800-50259600	Bivalent/Poised TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr5:50258800-50259600	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
11	chr5:50258800-50259600	Flanking Bivalent TSS/Enh	Primary T helper 17 cells PMA-I stimulated	--
12	chr5:50258800-50259600	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
13	chr5:50258800-50259600	Flanking Bivalent TSS/Enh	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr5:50258800-50259600	Flanking Bivalent TSS/Enh	Primary T killer naive cells fromperipheralblood	blood
15	chr5:50258800-50259600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr5:50258800-50259600	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
17	chr5:50258800-50259600	Active TSS	Hela-S3	cervix
18	chr5:50258800-50259600	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
19	chr5:50258800-50259800	Flanking Bivalent TSS/Enh	Primary T helper naive cells fromperipheralblood	blood
20	chr5:50258800-50259800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr5:50258800-50259800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr5:50258800-50260000	Bivalent/Poised TSS	Brain Anterior Caudate	brain
23	chr5:50258800-50260000	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
24	chr5:50258800-50260000	Bivalent/Poised TSS	Fetal Brain Female	brain
25	chr5:50258800-50260200	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr5:50258800-50260200	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
27	chr5:50258800-50260400	Active TSS	Right Atrium	heart
28	chr5:50259000-50259200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr5:50259000-50259200	Flanking Bivalent TSS/Enh	Primary B cells from cord blood	blood
30	chr5:50259000-50259200	Flanking Bivalent TSS/Enh	Primary T helper memory cells from peripheral blood 2	blood
31	chr5:50259000-50259200	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
32	chr5:50259000-50259200	Flanking Bivalent TSS/Enh	Esophagus	oesophagus
33	chr5:50259000-50259200	Flanking Bivalent TSS/Enh	Fetal Brain Male	brain
34	chr5:50259000-50259200	Flanking Active TSS	Placenta	Placenta
35	chr5:50259000-50259200	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
36	chr5:50259000-50259200	Bivalent/Poised TSS	Small Intestine	intestine
37	chr5:50259000-50259200	Enhancers	Spleen	Spleen
38	chr5:50259000-50259200	Bivalent Enhancer	HepG2	liver
39	chr5:50259000-50259200	Bivalent/Poised TSS	HMEC	breast
40	chr5:50259000-50259200	Flanking Bivalent TSS/Enh	HSMMtube	muscle
41	chr5:50259000-50259200	Flanking Active TSS	Osteobl	bone
42	chr5:50259000-50259400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr5:50259000-50259400	Bivalent/Poised TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr5:50259000-50259400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr5:50259000-50259400	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
46	chr5:50259000-50259400	Flanking Active TSS	Primary hematopoietic stem cells	blood
47	chr5:50259000-50259400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
48	chr5:50259000-50259400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr5:50259000-50259400	Flanking Bivalent TSS/Enh	Muscle Satellite Cultured Cells	--
50	chr5:50259000-50259400	Flanking Active TSS	Liver	Liver

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