Variant report

Variant	rs56246849
Chromosome Location	chr5:98367952-98367953
allele	A/G
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:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:98241392..98242207-chr5:98367928..98368798,4	MCF-7	breast:
2	chr5:98263162..98264704-chr5:98365544..98368385,2	K562	blood:
3	chr5:98362205..98363958-chr5:98366950..98369649,2	MCF-7	breast:
4	chr5:98241190..98242629-chr5:98367641..98368871,16	K562	blood:
5	chr5:98240910..98242219-chr5:98367905..98368817,11	MCF-7	breast:
6	chr5:98263067..98265701-chr5:98365532..98368540,4	MCF-7	breast:
7	chr5:98271965..98274046-chr5:98366756..98368349,2	K562	blood:
8	chr5:98265027..98268409-chr5:98365166..98367986,4	K562	blood:
9	chr5:98367873..98368452-chr5:98395154..98396281,3	MCF-7	breast:
10	chr5:98261108..98266251-chr5:98365242..98369850,9	K562	blood:
11	chr5:98356545..98359049-chr5:98366364..98368367,2	K562	blood:
12	chr5:98263884..98265572-chr5:98366799..98368375,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000248489	Chromatin interaction
ENSG00000200351	Chromatin interaction
ENSG00000153922	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10039507	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10040675	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10041263	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10041335	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10054523	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10055595	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10056842	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10056918	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10061406	0.93[EUR][1000 genomes]
rs10062455	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10064594	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10065808	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10067635	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10067866	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10068003	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10068917	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10077697	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10085106	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10085145	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10479350	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10479351	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10479352	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10479353	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10479354	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12332280	0.96[EUR][1000 genomes]
rs12332340	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12332364	0.93[EUR][1000 genomes]
rs12332383	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs161742	0.93[EUR][1000 genomes]
rs17166414	0.85[EUR][1000 genomes]
rs17166423	0.85[EUR][1000 genomes]
rs17166439	0.85[EUR][1000 genomes]
rs17166455	0.87[EUR][1000 genomes]
rs17166484	0.91[EUR][1000 genomes]
rs17166575	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17166578	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2164986	0.85[EUR][1000 genomes]
rs28555343	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28656032	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2963709	0.91[EUR][1000 genomes]
rs327810	0.81[EUR][1000 genomes]
rs36011435	0.85[EUR][1000 genomes]
rs44070	0.93[EUR][1000 genomes]
rs55780476	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55821667	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55854720	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56046686	0.89[AFR][1000 genomes]
rs56086412	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56096102	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56115002	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56153113	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56159022	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56160758	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56311403	0.91[AFR][1000 genomes]
rs56331326	0.80[EUR][1000 genomes]
rs56331947	0.91[EUR][1000 genomes]
rs56400831	0.85[EUR][1000 genomes]
rs58479016	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs58771325	0.89[EUR][1000 genomes]
rs6596659	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6867271	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6883467	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6885458	0.81[AFR][1000 genomes]
rs6890358	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6895358	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7708436	0.91[EUR][1000 genomes]
rs7719375	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7737402	0.93[EUR][1000 genomes]
rs9327950	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9327954	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9327955	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][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	nsv1024391	chr5:98355665-98653657	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
2	nsv599118	chr5:98358191-99029453	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv599119	chr5:98358191-99315677	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:98357400-98368400	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr5:98360200-98369000	Enhancers	Primary B cells from peripheral blood	blood
3	chr5:98361200-98368000	Weak transcription	Osteobl	bone
4	chr5:98362200-98368400	Weak transcription	Small Intestine	intestine
5	chr5:98362400-98368400	Weak transcription	Brain Hippocampus Middle	brain
6	chr5:98362800-98368400	Weak transcription	Duodenum Mucosa	Duodenum
7	chr5:98363200-98368400	Weak transcription	Fetal Intestine Large	intestine
8	chr5:98363400-98368000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr5:98363400-98368000	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr5:98363400-98368000	Weak transcription	Fetal Kidney	kidney
11	chr5:98363400-98368000	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr5:98363400-98368200	Weak transcription	Fetal Intestine Small	intestine
13	chr5:98363400-98368200	Weak transcription	Stomach Mucosa	stomach
14	chr5:98363400-98368400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr5:98363400-98368400	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr5:98363600-98368000	Weak transcription	Adipose Nuclei	Adipose
17	chr5:98363600-98368000	Weak transcription	A549	lung
18	chr5:98363600-98368400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr5:98363600-98368400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr5:98363600-98368600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr5:98364200-98368000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr5:98364200-98368000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr5:98364200-98368200	Weak transcription	Primary neutrophils fromperipheralblood	blood
24	chr5:98364400-98368200	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr5:98364400-98368200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr5:98364400-98368600	Enhancers	Primary B cells from cord blood	blood
27	chr5:98364600-98368200	Weak transcription	Primary T cells from cord blood	blood
28	chr5:98366200-98368400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr5:98366200-98368400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
30	chr5:98366200-98369400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr5:98366400-98368400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
32	chr5:98366400-98368600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
33	chr5:98366800-98368000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr5:98366800-98368000	Weak transcription	Thymus	Thymus
35	chr5:98366800-98368200	Weak transcription	Primary hematopoietic stem cells	blood
36	chr5:98366800-98368200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr5:98366800-98368200	Enhancers	Monocytes-CD14+_RO01746	blood
38	chr5:98366800-98368400	Enhancers	K562	blood
39	chr5:98366800-98368600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr5:98367000-98368200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr5:98367000-98368400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr5:98367000-98368400	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr5:98367200-98368000	Weak transcription	Fetal Thymus	thymus
44	chr5:98367200-98368200	Weak transcription	Primary T helper cells fromperipheralblood	blood
45	chr5:98367200-98368600	Enhancers	Primary T killer memory cells from peripheral blood	blood
46	chr5:98367200-98368600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr5:98367400-98368200	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr5:98367600-98368400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr5:98367600-98368400	Enhancers	Primary T helper cells PMA-I stimulated	--
50	chr5:98367600-98368400	Enhancers	HSMM	muscle

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