Variant report

Variant	rs962384
Chromosome Location	chr4:102181744-102181745
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	chr4:102176705..102178742-chr4:102180562..102183503,2	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	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1561719	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2028475	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2099813	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2583400	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2583401	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2583402	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2583406	0.93[EUR][1000 genomes]
rs2583410	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2850332	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2850339	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2850344	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2850348	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2850349	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2850350	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2850351	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2850352	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2850354	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2850355	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2850356	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2850357	0.93[EUR][1000 genomes]
rs2850358	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2850360	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2850954	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2850963	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2850967	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2850969	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2850974	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2850975	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2850976	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs755961	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs920559	0.89[EUR][1000 genomes]
rs920560	0.95[EUR][1000 genomes];0.87[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:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:102174200-102186000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr4:102174400-102185800	Weak transcription	HMEC	breast
3	chr4:102177800-102185000	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr4:102178000-102181800	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr4:102178000-102186600	Weak transcription	Brain Substantia Nigra	brain
6	chr4:102178200-102182200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr4:102178200-102183000	Weak transcription	Stomach Mucosa	stomach
8	chr4:102178200-102183800	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr4:102179000-102186800	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr4:102179200-102181800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
11	chr4:102179600-102181800	Enhancers	Primary B cells from cord blood	blood
12	chr4:102179600-102182400	Enhancers	A549	lung
13	chr4:102179800-102182600	Enhancers	Colon Smooth Muscle	Colon
14	chr4:102180200-102185800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr4:102180400-102181800	Enhancers	NH-A	brain
16	chr4:102180400-102183800	Weak transcription	Small Intestine	intestine
17	chr4:102180600-102182000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr4:102180600-102182000	Enhancers	NHLF	lung
19	chr4:102180600-102183800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr4:102180600-102185400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr4:102180600-102185800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr4:102180600-102186200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr4:102180600-102186200	Weak transcription	Pancreas	Pancrea
24	chr4:102180600-102191000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr4:102180600-102192400	Weak transcription	Ovary	ovary
26	chr4:102180600-102197000	Weak transcription	Left Ventricle	heart
27	chr4:102180600-102203000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr4:102180800-102182000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr4:102180800-102182000	Weak transcription	Fetal Heart	heart
30	chr4:102180800-102182200	Enhancers	NHEK	skin
31	chr4:102180800-102182600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr4:102180800-102186200	Weak transcription	Gastric	stomach
33	chr4:102181000-102181800	Enhancers	Osteobl	bone
34	chr4:102181000-102182000	Enhancers	Rectal Smooth Muscle	rectum
35	chr4:102181000-102182600	Enhancers	Adipose Nuclei	Adipose
36	chr4:102181000-102182600	Enhancers	Fetal Kidney	kidney
37	chr4:102181200-102181800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr4:102181200-102182200	Enhancers	Brain Anterior Caudate	brain
39	chr4:102181200-102183800	Weak transcription	Primary hematopoietic stem cells	blood
40	chr4:102181200-102183800	Weak transcription	Psoas Muscle	Psoas
41	chr4:102181200-102183800	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr4:102181200-102184000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr4:102181200-102185800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr4:102181200-102186600	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr4:102181200-102186800	Weak transcription	Primary T helper cells PMA-I stimulated	--
46	chr4:102181400-102182200	Weak transcription	Brain Hippocampus Middle	brain
47	chr4:102181400-102182400	Enhancers	Skeletal Muscle Male	skeletal muscle
48	chr4:102181400-102182800	Weak transcription	Primary B cells from peripheral blood	blood
49	chr4:102181400-102183200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
50	chr4:102181400-102184000	Weak transcription	Primary T helper cells fromperipheralblood	blood

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