Variant report

Variant	rs1684456
Chromosome Location	chr3:196351663-196351664
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:196349709..196351870-chr3:196352083..196353674,2	MCF-7	breast:
2	chr3:196334981..196337035-chr3:196350355..196352055,2	K562	blood:
3	chr3:196350969..196354463-chr3:196357895..196360563,3	MCF-7	breast:
4	chr3:196350963..196353680-chr3:196361979..196365286,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000232065	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs1552321	0.93[ASN][1000 genomes]
rs1825471	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2054745	0.87[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap];0.91[ASN][1000 genomes]
rs4346577	0.85[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs4591526	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap];0.91[ASN][1000 genomes]
rs6779465	0.90[CHB][hapmap];0.90[CHD][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs7426670	0.90[ASN][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	nsv1003066	chr3:196098763-196414159	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv948681	chr3:196148055-197007546	Weak transcription Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
3	nsv1014692	chr3:196242249-196531824	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
4	nsv878187	chr3:196245603-196554790	Enhancers ZNF genes & repeats Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
5	nsv491864	chr3:196263064-196468533	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
6	nsv829828	chr3:196268121-196463641	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
7	nsv1010643	chr3:196288064-196788645	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
8	nsv878188	chr3:196312124-196553867	Weak transcription Genic enhancers Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
9	nsv1003135	chr3:196348721-196738953	Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:196339600-196354800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
2	chr3:196347200-196354200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr3:196347400-196354000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr3:196347600-196354800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr3:196347600-196358200	Weak transcription	Colon Smooth Muscle	Colon
6	chr3:196347600-196358400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr3:196347600-196358400	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr3:196347600-196358400	Weak transcription	Fetal Intestine Small	intestine
9	chr3:196348400-196354800	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr3:196348600-196354000	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr3:196348600-196354800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr3:196349600-196352800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
13	chr3:196350000-196351800	Enhancers	Brain Hippocampus Middle	brain
14	chr3:196350000-196352400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr3:196350200-196352200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
16	chr3:196350200-196352200	Enhancers	Brain Substantia Nigra	brain
17	chr3:196350600-196358600	Weak transcription	Lung	lung
18	chr3:196350600-196358600	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr3:196350800-196352000	Flanking Active TSS	Primary B cells from cord blood	blood
20	chr3:196351000-196351800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr3:196351000-196351800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
22	chr3:196351000-196351800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
23	chr3:196351000-196352000	Flanking Active TSS	Primary hematopoietic stem cells	blood
24	chr3:196351000-196352000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
25	chr3:196351000-196352000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
26	chr3:196351000-196352000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr3:196351000-196352200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
28	chr3:196351200-196351800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
29	chr3:196351200-196351800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
30	chr3:196351200-196351800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
31	chr3:196351200-196351800	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
32	chr3:196351200-196351800	Active TSS	Duodenum Smooth Muscle	Duodenum
33	chr3:196351200-196351800	Flanking Active TSS	Fetal Thymus	thymus
34	chr3:196351200-196351800	Flanking Active TSS	Thymus	Thymus
35	chr3:196351200-196351800	Enhancers	Dnd41	blood
36	chr3:196351200-196352200	Active TSS	Duodenum Mucosa	Duodenum
37	chr3:196351200-196352200	Flanking Active TSS	GM12878-XiMat	blood
38	chr3:196351200-196352400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr3:196351200-196352400	Enhancers	Brain Cingulate Gyrus	brain
40	chr3:196351200-196352800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
41	chr3:196351200-196353800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr3:196351400-196351800	Flanking Active TSS	Primary B cells from peripheral blood	blood
43	chr3:196351400-196351800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
44	chr3:196351400-196351800	Active TSS	Primary T regulatory cells fromperipheralblood	blood
45	chr3:196351400-196351800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
46	chr3:196351400-196351800	Active TSS	Adipose Nuclei	Adipose
47	chr3:196351400-196351800	Flanking Active TSS	Brain Anterior Caudate	brain
48	chr3:196351400-196351800	Active TSS	Rectal Mucosa Donor 29	rectum
49	chr3:196351400-196351800	Active TSS	Rectal Smooth Muscle	rectum
50	chr3:196351400-196352400	Enhancers	Spleen	Spleen

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