Variant report

Variant	rs28517277
Chromosome Location	chr3:150134451-150134452
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:150133493..150135633-chr3:150263328..150264884,2	MCF-7	breast:
2	chr3:150100256..150103024-chr3:150133786..150136650,2	K562	blood:
3	chr3:149955070..149958943-chr3:150133193..150137279,5	MCF-7	breast:
4	chr3:150133801..150136735-chr3:150211220..150213846,2	MCF-7	breast:
5	chr3:150132083..150135574-chr3:150261466..150265454,4	K562	blood:

Variant related genes	Relation type
ENSG00000120742	Chromatin interaction
ENSG00000144895	Chromatin interaction
ENSG00000244541	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10513374	0.90[AFR][1000 genomes]
rs11711035	0.90[AFR][1000 genomes]
rs11719654	0.81[ASN][1000 genomes]
rs12054166	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12629077	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13069723	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13092207	0.81[ASN][1000 genomes]
rs13092341	0.89[ASN][1000 genomes]
rs13099758	0.90[AFR][1000 genomes]
rs16862648	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28587425	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28672230	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs33988810	0.81[ASN][1000 genomes]
rs34192407	0.81[ASN][1000 genomes]
rs34384576	0.92[ASN][1000 genomes]
rs34616287	0.88[ASN][1000 genomes]
rs35704634	0.89[ASN][1000 genomes]
rs35725711	0.88[ASN][1000 genomes]
rs4423794	0.86[AFR][1000 genomes]
rs4681206	0.90[AFR][1000 genomes]
rs4681618	0.90[AFR][1000 genomes]
rs56040746	0.81[ASN][1000 genomes]
rs62269065	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6440677	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6763024	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs879634	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9682043	0.85[ASN][1000 genomes]
rs9838366	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9865031	0.88[AFR][1000 genomes]
rs9875882	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv829755	chr3:149992023-150156001	Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	esv1828464	chr3:150096071-150149868	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv877645	chr3:150103135-150212698	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
4	esv1799287	chr3:150125721-150147118	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:150125000-150137400	Active TSS	GM12878-XiMat	blood
2	chr3:150131000-150136000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr3:150131000-150138600	Weak transcription	Lung	lung
4	chr3:150131000-150152000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr3:150131000-150166000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr3:150131200-150135200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr3:150131200-150138600	Enhancers	Colon Smooth Muscle	Colon
8	chr3:150131400-150138600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr3:150131800-150136000	Strong transcription	Primary B cells from peripheral blood	blood
10	chr3:150132000-150136200	Transcr. at gene 5' and 3'	K562	blood
11	chr3:150132200-150136000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
12	chr3:150132200-150136400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
13	chr3:150132200-150140600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
14	chr3:150132400-150134600	Enhancers	Rectal Smooth Muscle	rectum
15	chr3:150132400-150135000	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr3:150132400-150135800	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr3:150132400-150135800	Weak transcription	Ovary	ovary
18	chr3:150132400-150139200	Weak transcription	Fetal Stomach	stomach
19	chr3:150132400-150146000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr3:150132400-150151400	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr3:150132400-150151600	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr3:150132400-150159200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr3:150132400-150160400	Weak transcription	Pancreas	Pancrea
24	chr3:150132400-150175000	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr3:150132400-150175000	Weak transcription	Placenta	Placenta
26	chr3:150132600-150134600	Enhancers	Stomach Mucosa	stomach
27	chr3:150132600-150134800	Enhancers	Primary T helper cells fromperipheralblood	blood
28	chr3:150132600-150136200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
29	chr3:150132600-150136400	Genic enhancers	A549	lung
30	chr3:150132600-150137800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
31	chr3:150132600-150145200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr3:150132800-150134800	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr3:150132800-150135400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr3:150132800-150136600	Enhancers	Brain Angular Gyrus	brain
35	chr3:150132800-150138200	Enhancers	Brain Substantia Nigra	brain
36	chr3:150132800-150145800	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr3:150132800-150145800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr3:150132800-150151000	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr3:150133000-150134800	Enhancers	Brain Hippocampus Middle	brain
40	chr3:150133000-150136000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr3:150133000-150136400	Enhancers	Primary T killer memory cells from peripheral blood	blood
42	chr3:150133000-150136400	Genic enhancers	Fetal Lung	lung
43	chr3:150133000-150139800	Weak transcription	Fetal Kidney	kidney
44	chr3:150133200-150134800	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr3:150133400-150134600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr3:150133400-150134600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr3:150133400-150135800	Enhancers	Primary T helper naive cells from peripheral blood	blood
48	chr3:150133400-150136200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr3:150133400-150136200	Genic enhancers	NHEK	skin
50	chr3:150133400-150136600	Weak transcription	HUES64 Cell Line	embryonic stem cell

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