Variant report

Variant	rs6531943
Chromosome Location	chr4:87907563-87907564
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:87907221..87909869-chr4:87913541..87915799,2	K562	blood:
2	chr4:87906047..87909235-chr4:87925490..87928515,3	K562	blood:
3	chr4:87906409..87908323-chr4:87926209..87928101,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000172493	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10003332	0.95[ASN][1000 genomes]
rs10008600	0.97[ASN][1000 genomes]
rs10022960	0.95[ASN][1000 genomes]
rs1374936	0.85[ASN][1000 genomes]
rs1374937	0.85[ASN][1000 genomes]
rs168161	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17012291	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1972969	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2053772	0.97[ASN][1000 genomes]
rs2053774	0.93[ASN][1000 genomes]
rs2272777	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2705617	0.85[ASN][1000 genomes]
rs340627	0.95[ASN][1000 genomes]
rs340628	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs340629	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs340631	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs340632	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs340635	0.97[ASN][1000 genomes]
rs340640	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs340644	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs340645	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs340646	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs340647	0.95[ASN][1000 genomes]
rs340649	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs340652	0.97[ASN][1000 genomes]
rs4536897	0.95[ASN][1000 genomes]
rs4693155	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4693797	0.85[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs4693799	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58317309	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6531944	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6531945	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6531947	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6815546	0.81[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs6848056	0.90[ASN][1000 genomes]
rs6853011	0.95[ASN][1000 genomes]
rs73837575	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs895740	0.85[ASN][1000 genomes]
rs965824	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009937	chr4:87795314-88008345	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
2	nsv999176	chr4:87869996-88098136	Strong transcription Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers 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 target site	27 gene(s)	inside rSNPs	diseases
3	nsv998335	chr4:87869996-88104414	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv1001017	chr4:87872160-88087003	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv537166	chr4:87872160-88087003	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv999098	chr4:87899091-88016048	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription 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	25 gene(s)	inside rSNPs	diseases
7	nsv537167	chr4:87899091-88016048	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 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	chr4:87872600-87926200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr4:87882600-87920200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr4:87882800-87912400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr4:87892400-87920600	Weak transcription	Stomach Smooth Muscle	stomach
5	chr4:87892800-87909400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr4:87894400-87911000	Weak transcription	Pancreas	Pancrea
7	chr4:87894600-87915600	Weak transcription	Lung	lung
8	chr4:87894600-87921000	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr4:87895200-87909400	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr4:87895400-87920000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr4:87896200-87916000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr4:87896200-87919200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr4:87896800-87918800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr4:87897600-87915600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr4:87898200-87915400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr4:87899000-87915400	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr4:87899000-87915400	Weak transcription	Left Ventricle	heart
18	chr4:87899000-87920600	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr4:87899000-87921200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr4:87899200-87911000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr4:87899200-87913200	Weak transcription	Liver	Liver
22	chr4:87899200-87920800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr4:87899200-87922800	Weak transcription	Osteobl	bone
24	chr4:87899200-87925800	Weak transcription	Hela-S3	cervix
25	chr4:87899200-87926600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr4:87900000-87915600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr4:87900000-87924400	Weak transcription	NHEK	skin
28	chr4:87900200-87908200	Weak transcription	Stomach Mucosa	stomach
29	chr4:87900200-87920800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr4:87901000-87913000	Weak transcription	Fetal Intestine Large	intestine
31	chr4:87901200-87913200	Weak transcription	HepG2	liver
32	chr4:87903200-87918800	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr4:87903200-87926200	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr4:87903400-87908400	Weak transcription	GM12878-XiMat	blood
35	chr4:87903400-87909600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr4:87903400-87915400	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr4:87903600-87911400	Weak transcription	K562	blood
38	chr4:87903600-87915400	Weak transcription	Thymus	Thymus
39	chr4:87903600-87915400	Weak transcription	Dnd41	blood
40	chr4:87903600-87919800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr4:87903600-87921000	Weak transcription	Primary T cells from cord blood	blood
42	chr4:87903800-87907600	Weak transcription	Primary T helper cells PMA-I stimulated	--
43	chr4:87903800-87913000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr4:87903800-87915600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr4:87903800-87919800	Weak transcription	Primary T helper cells fromperipheralblood	blood
46	chr4:87903800-87920000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr4:87904000-87915200	Weak transcription	Fetal Thymus	thymus
48	chr4:87904200-87909400	Weak transcription	Primary hematopoietic stem cells	blood
49	chr4:87904200-87926200	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr4:87904400-87909400	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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