Variant report

Variant	rs277628
Chromosome Location	chr3:100055146-100055147
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:100055078-100055165	HepG2	liver:	n/a	n/a
2	POLR2A	chr3:100055110-100055249	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:100055058..100056849-chr3:100060980..100063043,2	MCF-7	breast:
2	chr3:100052434..100055247-chr3:100118351..100122265,5	K562	blood:
3	chr3:100051539..100055958-chr3:100056037..100061247,9	MCF-7	breast:
4	chr3:100052074..100055881-chr3:100116822..100121530,5	MCF-7	breast:

Variant related genes	Relation type
NIT2	TF binding region
ENSG00000114021	Chromatin interaction
ENSG00000154174	Chromatin interaction
ENSG00000206535	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10936180	0.91[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1123578	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1214380	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1214381	0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1228184	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12495001	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs1530283	0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs166747	0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs277620	0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs277622	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs277623	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs277626	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs277629	0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs277630	0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs277633	0.91[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs277634	0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs277635	0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs277638	0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs277642	0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs277644	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs277651	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs372438	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3772692	0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs3806615	0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs392066	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs402870	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs413425	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs431069	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs432715	0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6780662	0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs6791102	0.85[ASN][1000 genomes]
rs6794955	0.91[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7616634	0.91[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7641630	0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916476	chr3:99478229-100124625	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv1003924	chr3:99933762-100112690	Strong transcription Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:100054000-100065000	Weak transcription	Spleen	Spleen
2	chr3:100054200-100055200	Flanking Active TSS	Fetal Intestine Large	intestine
3	chr3:100054200-100081000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:100054400-100055200	Active TSS	Brain Germinal Matrix	brain
5	chr3:100054400-100067600	Weak transcription	Psoas Muscle	Psoas
6	chr3:100054600-100055200	Enhancers	Fetal Muscle Leg	muscle
7	chr3:100054600-100055200	Enhancers	Placenta	Placenta
8	chr3:100054600-100055200	Enhancers	HepG2	liver
9	chr3:100054600-100056000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
10	chr3:100054600-100056600	Enhancers	Fetal Intestine Small	intestine
11	chr3:100054600-100057000	Weak transcription	Primary hematopoietic stem cells	blood
12	chr3:100054600-100057000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr3:100054600-100057200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr3:100054600-100057200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr3:100054600-100057400	Weak transcription	Primary T cells from cord blood	blood
16	chr3:100054600-100058000	Weak transcription	Fetal Brain Male	brain
17	chr3:100054600-100058000	Weak transcription	Fetal Brain Female	brain
18	chr3:100054600-100058200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr3:100054600-100058400	Weak transcription	Brain Cingulate Gyrus	brain
20	chr3:100054600-100058600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr3:100054600-100058600	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr3:100054600-100058800	Weak transcription	Aorta	Aorta
23	chr3:100054600-100059400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr3:100054600-100059800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr3:100054600-100060200	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr3:100054600-100063000	Weak transcription	Brain Substantia Nigra	brain
27	chr3:100054600-100064200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr3:100054600-100064400	Weak transcription	Thymus	Thymus
29	chr3:100054600-100102600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr3:100054800-100055200	Enhancers	ES-I3 Cell Line	embryonic stem cell
31	chr3:100054800-100055200	Enhancers	HMEC	breast
32	chr3:100054800-100055200	Enhancers	K562	blood
33	chr3:100054800-100055800	Enhancers	HUES64 Cell Line	embryonic stem cell
34	chr3:100054800-100056600	Weak transcription	Fetal Stomach	stomach
35	chr3:100054800-100057000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr3:100054800-100057000	Weak transcription	Fetal Lung	lung
37	chr3:100054800-100057000	Weak transcription	Fetal Muscle Trunk	muscle
38	chr3:100054800-100057200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr3:100054800-100057200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr3:100054800-100057200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr3:100054800-100057200	Weak transcription	Primary B cells from cord blood	blood
42	chr3:100054800-100057200	Weak transcription	HSMM	muscle
43	chr3:100054800-100057200	Weak transcription	Osteobl	bone
44	chr3:100054800-100057400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr3:100054800-100057400	Weak transcription	Monocytes-CD14+_RO01746	blood
46	chr3:100054800-100057600	Weak transcription	Primary B cells from peripheral blood	blood
47	chr3:100054800-100057600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr3:100054800-100057600	Weak transcription	Adipose Nuclei	Adipose
49	chr3:100054800-100057600	Weak transcription	Brain Hippocampus Middle	brain
50	chr3:100054800-100057600	Weak transcription	Rectal Mucosa Donor 29	rectum

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