Variant report

Variant	rs9878250
Chromosome Location	chr3:53918947-53918948
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:53913333..53919757-chr3:53920203..53928086,26	K562	blood:
2	chr3:53914775..53921125-chr3:53923203..53927129,12	MCF-7	breast:
3	chr3:53906811..53909807-chr3:53917602..53920226,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000113812	Chromatin interaction
ENSG00000113811	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs11130383	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11130384	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11562	0.83[AFR][1000 genomes]
rs12715465	1.00[AMR][1000 genomes]
rs13321898	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13322337	1.00[AMR][1000 genomes]
rs13434145	1.00[AMR][1000 genomes]
rs28409957	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6782007	1.00[AMR][1000 genomes]
rs6785238	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6802878	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72556356	1.00[AMR][1000 genomes]
rs7614233	1.00[AMR][1000 genomes]
rs7636496	1.00[AMR][1000 genomes]
rs7637908	1.00[AMR][1000 genomes]
rs7640840	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9814675	1.00[AMR][1000 genomes]
rs9816010	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9818571	1.00[AMR][1000 genomes]
rs9823141	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9830672	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9833359	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9834168	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9835258	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9849610	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9852243	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9859937	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9860224	1.00[AMR][1000 genomes]
rs9872403	1.00[AMR][1000 genomes]
rs9882134	0.91[AFR][1000 genomes];1.00[AMR][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	nsv1003621	chr3:53448934-54425322	Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv1001128	chr3:53659570-53927842	Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1013783	chr3:53694418-53934781	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv876804	chr3:53833509-53934171	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	nsv1010575	chr3:53846741-53934781	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
6	nsv1006990	chr3:53849510-54285212	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
7	nsv997771	chr3:53852695-53926635	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
8	nsv1002141	chr3:53858541-53934781	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
9	nsv1014752	chr3:53912429-54123246	Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 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	chr3:53916200-53919400	Weak transcription	Spleen	Spleen
2	chr3:53916200-53924800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr3:53916200-53924800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:53916600-53919200	Weak transcription	Colonic Mucosa	Colon
5	chr3:53916600-53919400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr3:53916600-53921000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr3:53916600-53921800	Strong transcription	HSMM	muscle
8	chr3:53916600-53922000	Weak transcription	K562	blood
9	chr3:53916600-53923400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr3:53916600-53924000	Weak transcription	Psoas Muscle	Psoas
11	chr3:53916600-53924000	Weak transcription	A549	lung
12	chr3:53916600-53924400	Weak transcription	Fetal Kidney	kidney
13	chr3:53916600-53924800	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr3:53916600-53924800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr3:53916600-53924800	Weak transcription	Aorta	Aorta
16	chr3:53916800-53919400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr3:53916800-53919400	Weak transcription	HSMMtube	muscle
18	chr3:53916800-53919400	Weak transcription	NHEK	skin
19	chr3:53916800-53920000	Weak transcription	Primary T cells from cord blood	blood
20	chr3:53916800-53920800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr3:53916800-53921000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr3:53916800-53921200	Weak transcription	HepG2	liver
23	chr3:53916800-53922000	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr3:53916800-53922000	Weak transcription	Fetal Heart	heart
25	chr3:53916800-53923200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr3:53916800-53923200	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr3:53916800-53923400	Weak transcription	Fetal Brain Male	brain
28	chr3:53916800-53924000	Weak transcription	Stomach Mucosa	stomach
29	chr3:53916800-53924400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr3:53916800-53924600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr3:53916800-53924600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr3:53917000-53919400	Strong transcription	Brain Hippocampus Middle	brain
33	chr3:53917000-53920000	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr3:53917000-53921400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr3:53917000-53922000	Weak transcription	Brain Substantia Nigra	brain
36	chr3:53917000-53922400	Strong transcription	Brain Germinal Matrix	brain
37	chr3:53917000-53922800	Strong transcription	Primary T cells fromperipheralblood	blood
38	chr3:53917000-53923600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr3:53917200-53920000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr3:53917200-53920200	Strong transcription	Duodenum Smooth Muscle	Duodenum
41	chr3:53917200-53920400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr3:53917200-53920400	Strong transcription	Skeletal Muscle Female	skeletal muscle
43	chr3:53917200-53920400	Strong transcription	GM12878-XiMat	blood
44	chr3:53917200-53920800	Strong transcription	Fetal Intestine Small	intestine
45	chr3:53917200-53921200	Strong transcription	NHLF	lung
46	chr3:53917200-53921400	Strong transcription	Fetal Brain Female	brain
47	chr3:53917200-53921400	Strong transcription	Fetal Stomach	stomach
48	chr3:53917200-53921800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr3:53917200-53922000	Strong transcription	Rectal Mucosa Donor 29	rectum
50	chr3:53917200-53922200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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