Variant report

Variant	rs28516957
Chromosome Location	chr3:119620753-119620754
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:119619528..119621705-chr3:119622224..119624358,2	MCF-7	breast:
2	chr3:119619268..119620882-chr3:119812978..119815469,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000082701	Chromatin interaction
ENSG00000242622	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs11921053	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12494560	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13314595	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1579031	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16830689	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1719889	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1719895	0.84[ASN][1000 genomes]
rs1732165	0.84[ASN][1000 genomes]
rs1732169	0.84[ASN][1000 genomes]
rs2037547	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2461827	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3108749	0.84[ASN][1000 genomes]
rs334535	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs334559	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4072520	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4438691	0.84[ASN][1000 genomes]
rs4450859	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4688043	0.84[ASN][1000 genomes]
rs56126162	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs66650215	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6769435	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6770314	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6771023	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6774693	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6775397	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6779828	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6790751	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6795874	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6802301	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7613197	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7617372	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7620750	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7624540	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7636600	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7649661	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs7652172	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9289138	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9851174	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9859778	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9879992	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][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	nsv949589	chr3:119560606-120175917	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv829696	chr3:119567659-119711405	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv1001476	chr3:119575386-120075417	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
4	nsv536704	chr3:119575386-120075417	Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 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	chr3:119546000-119663400	Weak transcription	Lung	lung
2	chr3:119569400-119629400	Weak transcription	Esophagus	oesophagus
3	chr3:119574600-119631600	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr3:119582400-119624000	Weak transcription	Brain Germinal Matrix	brain
5	chr3:119582400-119626600	Weak transcription	Fetal Heart	heart
6	chr3:119582400-119629400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr3:119582600-119627200	Weak transcription	Fetal Muscle Trunk	muscle
8	chr3:119582600-119627400	Weak transcription	Right Ventricle	heart
9	chr3:119582800-119621200	Weak transcription	Fetal Intestine Large	intestine
10	chr3:119583600-119621400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr3:119583800-119630400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr3:119584000-119622800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr3:119597600-119659000	Weak transcription	Gastric	stomach
14	chr3:119603400-119624200	Weak transcription	Hela-S3	cervix
15	chr3:119603600-119624200	Weak transcription	HepG2	liver
16	chr3:119604800-119627800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr3:119608000-119621600	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr3:119608000-119627800	Weak transcription	Left Ventricle	heart
19	chr3:119608000-119643600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr3:119608200-119621200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr3:119608200-119621400	Weak transcription	Placenta	Placenta
22	chr3:119608200-119627400	Weak transcription	Thymus	Thymus
23	chr3:119608200-119639200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr3:119608200-119677800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr3:119608400-119629800	Weak transcription	Fetal Brain Female	brain
26	chr3:119608600-119621200	Weak transcription	Primary B cells from peripheral blood	blood
27	chr3:119608600-119622800	Weak transcription	Primary T helper cells PMA-I stimulated	--
28	chr3:119608600-119629200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr3:119608600-119630000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr3:119608600-119630000	Weak transcription	Fetal Muscle Leg	muscle
31	chr3:119608800-119629800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr3:119609000-119629600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr3:119609200-119630000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr3:119611200-119623400	Weak transcription	Duodenum Mucosa	Duodenum
35	chr3:119611200-119624000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr3:119611200-119630200	Weak transcription	Psoas Muscle	Psoas
37	chr3:119611200-119643400	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr3:119611200-119667000	Weak transcription	Pancreas	Pancrea
39	chr3:119611400-119622000	Weak transcription	Fetal Kidney	kidney
40	chr3:119611400-119622000	Weak transcription	A549	lung
41	chr3:119611400-119622600	Weak transcription	NH-A	brain
42	chr3:119611400-119624200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr3:119611400-119627400	Weak transcription	Brain Angular Gyrus	brain
44	chr3:119611400-119627400	Weak transcription	Brain Substantia Nigra	brain
45	chr3:119611400-119627600	Weak transcription	Brain Anterior Caudate	brain
46	chr3:119611400-119627800	Weak transcription	Aorta	Aorta
47	chr3:119611400-119627800	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr3:119611400-119629400	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr3:119611400-119629400	Weak transcription	Stomach Smooth Muscle	stomach
50	chr3:119611400-119630000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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