Variant report

Variant	rs6789088
Chromosome Location	chr3:194797968-194797969
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:194792659..194796226-chr3:194797531..194801408,5	MCF-7	breast:
2	chr3:194789447..194796347-chr3:194796697..194800807,6	K562	blood:
3	chr3:194782723..194784789-chr3:194796384..194799142,2	MCF-7	breast:
4	chr3:194797462..194799742-chr3:194801483..194805292,3	K562	blood:

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs56386553	1.00[AMR][1000 genomes]
rs61422283	1.00[AMR][1000 genomes]
rs6773392	1.00[AMR][1000 genomes]
rs6806859	1.00[AMR][1000 genomes]
rs6809483	1.00[AMR][1000 genomes]
rs73067087	1.00[AMR][1000 genomes]
rs73890627	1.00[AMR][1000 genomes]
rs73890636	1.00[AMR][1000 genomes]
rs73890648	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73890650	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73890665	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73890666	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73890713	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007697	chr3:194554814-195009930	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
2	nsv536873	chr3:194554814-195009930	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
3	nsv997779	chr3:194687093-194885936	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
4	nsv536874	chr3:194687093-194885936	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
5	nsv1009796	chr3:194737333-195124248	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
6	esv1813153	chr3:194754532-194851746	Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv878136	chr3:194779412-194845226	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:194779000-194808000	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr3:194780200-194800000	Weak transcription	Right Atrium	heart
3	chr3:194781000-194808000	Weak transcription	Colonic Mucosa	Colon
4	chr3:194783600-194801400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr3:194785400-194799200	Weak transcription	Pancreas	Pancrea
6	chr3:194785600-194801400	Weak transcription	Fetal Lung	lung
7	chr3:194785600-194801600	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr3:194785600-194802000	Weak transcription	Rectal Smooth Muscle	rectum
9	chr3:194786000-194800400	Weak transcription	GM12878-XiMat	blood
10	chr3:194787200-194800000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr3:194787600-194801000	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr3:194789800-194800000	Weak transcription	Primary hematopoietic stem cells	blood
13	chr3:194790400-194808000	Weak transcription	Primary T helper cells fromperipheralblood	blood
14	chr3:194790600-194798000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr3:194790600-194798200	Weak transcription	Aorta	Aorta
16	chr3:194790600-194800000	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr3:194790600-194800200	Weak transcription	Adipose Nuclei	Adipose
18	chr3:194790600-194800600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr3:194790600-194801000	Weak transcription	Brain Hippocampus Middle	brain
20	chr3:194790600-194801600	Weak transcription	Brain Cingulate Gyrus	brain
21	chr3:194790600-194801800	Weak transcription	Colon Smooth Muscle	Colon
22	chr3:194790600-194802000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr3:194790600-194802400	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr3:194790600-194807800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr3:194790800-194798600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr3:194790800-194799400	Weak transcription	Brain Germinal Matrix	brain
27	chr3:194790800-194799800	Weak transcription	Lung	lung
28	chr3:194790800-194800000	Weak transcription	HUVEC	blood vessel
29	chr3:194790800-194800400	Weak transcription	Fetal Brain Female	brain
30	chr3:194790800-194800600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr3:194790800-194800800	Weak transcription	Esophagus	oesophagus
32	chr3:194790800-194803600	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr3:194790800-194807400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr3:194790800-194807800	Weak transcription	HepG2	liver
35	chr3:194791000-194800400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr3:194791000-194801400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr3:194791000-194821800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr3:194791600-194799800	Weak transcription	Hela-S3	cervix
39	chr3:194791600-194800200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr3:194792000-194799200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr3:194792200-194800400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr3:194792400-194804200	Enhancers	Fetal Thymus	thymus
43	chr3:194793600-194801200	Weak transcription	Stomach Smooth Muscle	stomach
44	chr3:194793800-194799800	Weak transcription	Left Ventricle	heart
45	chr3:194793800-194800600	Weak transcription	Primary T cells from cord blood	blood
46	chr3:194794000-194799400	Weak transcription	Right Ventricle	heart
47	chr3:194794000-194800600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
48	chr3:194794000-194807800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
49	chr3:194794800-194804400	Enhancers	Spleen	Spleen
50	chr3:194795400-194799600	Weak transcription	Skeletal Muscle Female	skeletal muscle

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