Variant report

Variant	rs2028475
Chromosome Location	chr4:102176481-102176482
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	chr4:102171123..102173007-chr4:102176069..102177893,2	MCF-7	breast:

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1441433	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1561719	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2099813	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2583400	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2583401	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2583402	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2583406	0.94[EUR][1000 genomes]
rs2583410	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2850332	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2850339	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2850344	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2850348	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2850349	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2850350	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2850351	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2850352	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2850354	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2850355	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2850356	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2850357	0.94[EUR][1000 genomes]
rs2850358	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2850360	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2850954	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2850963	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2850967	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2850969	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2850974	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2850975	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2850976	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs755961	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs920559	0.88[EUR][1000 genomes]
rs920560	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs962384	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931418	chr4:101500167-102443207	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv999741	chr4:102009017-102454115	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
3	nsv537199	chr4:102009017-102454115	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1004766	chr4:102009017-102713765	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
5	nsv537200	chr4:102009017-102713765	Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
6	nsv1011351	chr4:102056024-102450302	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:102157800-102179600	Weak transcription	Primary B cells from cord blood	blood
2	chr4:102159200-102179800	Weak transcription	Psoas Muscle	Psoas
3	chr4:102161000-102177400	Weak transcription	Primary B cells from peripheral blood	blood
4	chr4:102161000-102177400	Weak transcription	Colon Smooth Muscle	Colon
5	chr4:102166200-102177400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr4:102166200-102179400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr4:102173200-102179400	Weak transcription	Primary hematopoietic stem cells	blood
8	chr4:102173400-102177200	Weak transcription	Brain Hippocampus Middle	brain
9	chr4:102174000-102181200	Weak transcription	Brain Anterior Caudate	brain
10	chr4:102174200-102177000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr4:102174200-102177200	Weak transcription	Brain Cingulate Gyrus	brain
12	chr4:102174200-102177400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr4:102174200-102177400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr4:102174200-102177600	Weak transcription	Small Intestine	intestine
15	chr4:102174200-102178800	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr4:102174200-102179400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr4:102174200-102179600	Weak transcription	Duodenum Mucosa	Duodenum
18	chr4:102174200-102179800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr4:102174200-102180000	Weak transcription	Left Ventricle	heart
20	chr4:102174200-102181000	Weak transcription	Adipose Nuclei	Adipose
21	chr4:102174200-102186000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr4:102174400-102177400	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr4:102174400-102177400	Weak transcription	HepG2	liver
24	chr4:102174400-102180000	Weak transcription	NHDF-Ad	bronchial
25	chr4:102174400-102180600	Weak transcription	NHLF	lung
26	chr4:102174400-102185800	Weak transcription	HMEC	breast
27	chr4:102174600-102177200	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr4:102174600-102177200	Weak transcription	A549	lung
29	chr4:102174600-102179800	Weak transcription	Ovary	ovary
30	chr4:102175000-102177000	Weak transcription	Stomach Mucosa	stomach
31	chr4:102175000-102177600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr4:102175200-102180000	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr4:102175400-102179800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr4:102175800-102179000	Enhancers	Pancreatic Islets	Pancreatic Islet
35	chr4:102175800-102180400	Weak transcription	NH-A	brain
36	chr4:102176000-102177400	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr4:102176000-102177800	Enhancers	iPS-20b Cell Line	embryonic stem cell
38	chr4:102176000-102178000	Enhancers	Rectal Mucosa Donor 29	rectum
39	chr4:102176000-102178200	Enhancers	iPS-18 Cell Line	embryonic stem cell
40	chr4:102176000-102178200	Enhancers	Rectal Mucosa Donor 31	rectum
41	chr4:102176000-102179600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr4:102176200-102176600	Flanking Active TSS	HUVEC	blood vessel
43	chr4:102176200-102176600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
44	chr4:102176200-102181000	Weak transcription	Fetal Kidney	kidney
45	chr4:102176400-102180400	Weak transcription	Skeletal Muscle Female	skeletal muscle

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