Variant report

Variant	rs28534411
Chromosome Location	chr4:102179957-102179958
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:102178495..102180212-chr4:102267850..102269476,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000138814	Chromatin interaction
ENSG00000254531	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10004830	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10015480	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10019627	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10027301	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17030915	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17030959	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17030989	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs28379119	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28421266	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs28464050	1.00[EUR][1000 genomes]
rs28491829	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28542998	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs28553282	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs28614035	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs28638143	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28640942	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28675750	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28723066	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs58084948	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs58598913	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs58898502	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72919782	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72919785	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9998913	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][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:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:102174000-102181200	Weak transcription	Brain Anterior Caudate	brain
2	chr4:102174200-102180000	Weak transcription	Left Ventricle	heart
3	chr4:102174200-102181000	Weak transcription	Adipose Nuclei	Adipose
4	chr4:102174200-102186000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr4:102174400-102180000	Weak transcription	NHDF-Ad	bronchial
6	chr4:102174400-102180600	Weak transcription	NHLF	lung
7	chr4:102174400-102185800	Weak transcription	HMEC	breast
8	chr4:102175200-102180000	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr4:102175800-102180400	Weak transcription	NH-A	brain
10	chr4:102176200-102181000	Weak transcription	Fetal Kidney	kidney
11	chr4:102176400-102180400	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr4:102177800-102180200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr4:102177800-102181000	Weak transcription	Brain Cingulate Gyrus	brain
14	chr4:102177800-102181600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr4:102177800-102185000	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr4:102178000-102181800	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr4:102178000-102186600	Weak transcription	Brain Substantia Nigra	brain
18	chr4:102178200-102180000	Weak transcription	Brain Hippocampus Middle	brain
19	chr4:102178200-102182200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr4:102178200-102183000	Weak transcription	Stomach Mucosa	stomach
21	chr4:102178200-102183800	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr4:102179000-102180000	Weak transcription	Fetal Heart	heart
23	chr4:102179000-102180600	Enhancers	Primary T killer memory cells from peripheral blood	blood
24	chr4:102179000-102186800	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr4:102179200-102181800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
26	chr4:102179400-102180000	Enhancers	Primary neutrophils fromperipheralblood	blood
27	chr4:102179400-102180200	Enhancers	Primary T cells from cord blood	blood
28	chr4:102179400-102180400	Enhancers	Small Intestine	intestine
29	chr4:102179400-102180600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr4:102179400-102180600	Enhancers	Primary hematopoietic stem cells	blood
31	chr4:102179400-102180600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
32	chr4:102179400-102180600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr4:102179400-102180600	Enhancers	Pancreas	Pancrea
34	chr4:102179400-102181200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
35	chr4:102179400-102181200	Enhancers	Primary T helper cells PMA-I stimulated	--
36	chr4:102179400-102181200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr4:102179400-102181200	Enhancers	Aorta	Aorta
38	chr4:102179400-102181400	Enhancers	Primary B cells from peripheral blood	blood
39	chr4:102179400-102181400	Enhancers	Primary T helper cells fromperipheralblood	blood
40	chr4:102179400-102181600	Enhancers	Primary hematopoietic stem cells short term culture	blood
41	chr4:102179600-102180200	Enhancers	Primary T helper naive cells from peripheral blood	blood
42	chr4:102179600-102180400	Enhancers	GM12878-XiMat	blood
43	chr4:102179600-102180600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
44	chr4:102179600-102180600	Enhancers	Duodenum Mucosa	Duodenum
45	chr4:102179600-102181000	Enhancers	HUVEC	blood vessel
46	chr4:102179600-102181800	Enhancers	Primary B cells from cord blood	blood
47	chr4:102179600-102182400	Enhancers	A549	lung
48	chr4:102179800-102180200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr4:102179800-102180600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
50	chr4:102179800-102180600	Enhancers	Ovary	ovary

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