Variant report

Variant	rs899346
Chromosome Location	chr3:140990784-140990785
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:140981939..140984087-chr3:140988677..140991086,2	MCF-7	breast:

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs16851272	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16851274	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28480447	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28671450	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4384928	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4596121	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4683590	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4683591	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56165506	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56192713	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59752258	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6794495	0.95[EUR][1000 genomes]
rs73869553	0.95[EUR][1000 genomes]
rs899345	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv460870	chr3:140938546-141005574	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv591892	chr3:140938546-141005574	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv877551	chr3:140970556-141029860	Flanking Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:140957400-141001000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr3:140959200-140998400	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr3:140961200-141012600	Weak transcription	Aorta	Aorta
4	chr3:140974800-140991400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr3:140975000-140993400	Weak transcription	Lung	lung
6	chr3:140975000-140993400	Weak transcription	Spleen	Spleen
7	chr3:140975200-140991800	Weak transcription	Placenta	Placenta
8	chr3:140975800-140993200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr3:140978000-140998000	Weak transcription	Rectal Smooth Muscle	rectum
10	chr3:140978200-140993600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr3:140978800-140993000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr3:140979000-141000800	Weak transcription	Fetal Kidney	kidney
13	chr3:140979000-141013200	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr3:140979800-140992800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr3:140980800-141005600	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr3:140981000-140998400	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr3:140981200-141013200	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr3:140981200-141013400	Weak transcription	Colonic Mucosa	Colon
19	chr3:140981400-141001000	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr3:140981600-140992000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr3:140981600-140993200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr3:140983000-140992000	Weak transcription	Brain Angular Gyrus	brain
23	chr3:140983600-141021600	Weak transcription	Esophagus	oesophagus
24	chr3:140983800-140993000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr3:140984000-140997400	Weak transcription	Fetal Brain Female	brain
26	chr3:140984200-141000800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr3:140984400-140992600	Weak transcription	Fetal Muscle Leg	muscle
28	chr3:140984600-140997600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr3:140984800-141006400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr3:140985200-140993000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr3:140985800-140993800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr3:140986200-140997600	Weak transcription	Brain Anterior Caudate	brain
33	chr3:140986200-140997600	Weak transcription	Brain Hippocampus Middle	brain
34	chr3:140986200-140997600	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr3:140986200-140998000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr3:140986200-141000800	Weak transcription	Fetal Lung	lung
37	chr3:140986400-140992800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr3:140986600-140994200	Weak transcription	Primary neutrophils fromperipheralblood	blood
39	chr3:140986600-140994400	Genic enhancers	Dnd41	blood
40	chr3:140986800-140992800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr3:140986800-140997400	Weak transcription	Primary monocytes fromperipheralblood	blood
42	chr3:140987200-140997400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr3:140987400-140990800	Strong transcription	Monocytes-CD14+_RO01746	blood
44	chr3:140987400-140992000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr3:140987400-140992600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr3:140987400-140992800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr3:140987600-140993600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr3:140987800-140992800	Weak transcription	Primary T cells fromperipheralblood	blood
49	chr3:140987800-140992800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
50	chr3:140987800-140993000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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