Variant report

Variant	rs6799977
Chromosome Location	chr3:196350841-196350842
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	chr3:196345698..196350992-chr3:196355970..196361124,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000232065	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs12718061	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12718062	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1385331	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34088166	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34515026	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3964454	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6583331	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6807839	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7614184	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9824819	0.82[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:61 , 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	chr3:196339800-196351000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr3:196343400-196351000	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr3:196344600-196351000	Weak transcription	Thymus	Thymus
5	chr3:196345400-196351200	Enhancers	Fetal Thymus	thymus
6	chr3:196346400-196351200	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr3:196346400-196351200	Weak transcription	Dnd41	blood
8	chr3:196346800-196351000	Enhancers	Primary neutrophils fromperipheralblood	blood
9	chr3:196347200-196351200	Weak transcription	Brain Cingulate Gyrus	brain
10	chr3:196347200-196351400	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr3:196347200-196354200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr3:196347400-196351000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr3:196347400-196351000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr3:196347400-196351200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr3:196347400-196351400	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr3:196347400-196354000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr3:196347600-196351000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr3:196347600-196351000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr3:196347600-196351000	Weak transcription	K562	blood
20	chr3:196347600-196351200	Enhancers	Primary hematopoietic stem cells short term culture	blood
21	chr3:196347600-196351200	Weak transcription	Duodenum Mucosa	Duodenum
22	chr3:196347600-196351200	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr3:196347600-196354800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr3:196347600-196358200	Weak transcription	Colon Smooth Muscle	Colon
25	chr3:196347600-196358400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr3:196347600-196358400	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr3:196347600-196358400	Weak transcription	Fetal Intestine Small	intestine
28	chr3:196347800-196351000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr3:196347800-196351400	Weak transcription	Rectal Smooth Muscle	rectum
30	chr3:196348400-196354800	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr3:196348600-196354000	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr3:196348600-196354800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr3:196349600-196352800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
34	chr3:196350000-196351800	Enhancers	Brain Hippocampus Middle	brain
35	chr3:196350000-196352400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr3:196350200-196351000	Enhancers	Primary hematopoietic stem cells	blood
37	chr3:196350200-196351000	Enhancers	Primary T helper cells PMA-I stimulated	--
38	chr3:196350200-196351200	Enhancers	Primary T cells from cord blood	blood
39	chr3:196350200-196351200	Enhancers	Primary T cells fromperipheralblood	blood
40	chr3:196350200-196351200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
41	chr3:196350200-196351200	Enhancers	Primary T helper cells fromperipheralblood	blood
42	chr3:196350200-196351400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr3:196350200-196351400	Enhancers	Cortex derived primary cultured neurospheres	brain
44	chr3:196350200-196351400	Enhancers	Brain Anterior Caudate	brain
45	chr3:196350200-196351600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr3:196350200-196351600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr3:196350200-196352200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
48	chr3:196350200-196352200	Enhancers	Brain Substantia Nigra	brain
49	chr3:196350400-196351000	Enhancers	Primary T helper naive cells from peripheral blood	blood
50	chr3:196350400-196351000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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