Variant report

Variant	rs73819633
Chromosome Location	chr4:56406685-56406686
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	chr4:56403772..56408020-chr4:56410640..56413640,7	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PDCL2-1	chr4:56406669-56407002	NONHSAT096474

Variant related genes	Relation type
ENSG00000134852	Chromatin interaction
ENSG00000272969	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10031586	1.00[EUR][1000 genomes]
rs1488940	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1533803	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1554482	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17085739	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17085769	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17085780	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17085821	1.00[EUR][1000 genomes]
rs2130039	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2140076	1.00[EUR][1000 genomes]
rs2412660	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs35150421	1.00[EUR][1000 genomes]
rs57219525	1.00[EUR][1000 genomes]
rs57848550	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58395965	1.00[EUR][1000 genomes]
rs6554272	1.00[EUR][1000 genomes]
rs6820823	1.00[EUR][1000 genomes]
rs6847415	1.00[EUR][1000 genomes]
rs6855837	1.00[EUR][1000 genomes]
rs73149762	1.00[EUR][1000 genomes]
rs73151873	1.00[EUR][1000 genomes]
rs73151889	1.00[EUR][1000 genomes]
rs73153687	1.00[EUR][1000 genomes]
rs73817206	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73819624	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73819626	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73819631	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73819635	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73819636	0.88[AFR][1000 genomes]
rs73819642	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73819647	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7655255	1.00[EUR][1000 genomes]
rs7693751	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3328582	chr4:56164136-56486156	Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	esv2755990	chr4:56317136-57143037	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
3	nsv10496	chr4:56336946-56841137	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:56361600-56411800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr4:56391600-56408800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr4:56391600-56409400	Weak transcription	NHDF-Ad	bronchial
4	chr4:56391800-56409400	Weak transcription	HMEC	breast
5	chr4:56391800-56409400	Weak transcription	NHEK	skin
6	chr4:56391800-56409600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr4:56393200-56408000	Weak transcription	K562	blood
8	chr4:56396800-56411600	Weak transcription	Psoas Muscle	Psoas
9	chr4:56399600-56411600	Weak transcription	Left Ventricle	heart
10	chr4:56399800-56411000	Weak transcription	Brain Substantia Nigra	brain
11	chr4:56400000-56410200	Weak transcription	Fetal Intestine Small	intestine
12	chr4:56400800-56406800	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr4:56400800-56409600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr4:56401000-56409400	Weak transcription	HSMM	muscle
15	chr4:56401000-56409600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr4:56401000-56411400	Weak transcription	Primary B cells from peripheral blood	blood
17	chr4:56401200-56410000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr4:56401200-56411800	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr4:56401600-56410200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr4:56402400-56409400	Weak transcription	Fetal Heart	heart
21	chr4:56402800-56409600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr4:56402800-56410600	Weak transcription	Primary hematopoietic stem cells	blood
23	chr4:56402800-56411600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr4:56403000-56411400	Weak transcription	Fetal Muscle Leg	muscle
25	chr4:56403200-56406800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr4:56403600-56408000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
27	chr4:56403800-56410400	Weak transcription	Fetal Stomach	stomach
28	chr4:56403800-56411800	Weak transcription	Lung	lung
29	chr4:56404200-56409400	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr4:56404600-56406800	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr4:56404600-56410200	Weak transcription	Fetal Lung	lung
32	chr4:56405000-56408800	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr4:56405000-56410000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr4:56405000-56411000	Weak transcription	Fetal Kidney	kidney
35	chr4:56405000-56411400	Weak transcription	Fetal Muscle Trunk	muscle
36	chr4:56405200-56407000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr4:56405200-56407200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr4:56405200-56410000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr4:56405200-56410800	Weak transcription	Monocytes-CD14+_RO01746	blood
40	chr4:56405400-56410000	Weak transcription	HepG2	liver
41	chr4:56405600-56406800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr4:56405600-56406800	Weak transcription	Pancreas	Pancrea
43	chr4:56405600-56407600	Weak transcription	Primary T cells from cord blood	blood
44	chr4:56405600-56407600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr4:56405600-56409400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr4:56405600-56409400	Weak transcription	Adipose Nuclei	Adipose
47	chr4:56405600-56410200	Weak transcription	Hela-S3	cervix
48	chr4:56405600-56410400	Weak transcription	Primary T helper cells fromperipheralblood	blood
49	chr4:56405600-56411400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr4:56405600-56411400	Weak transcription	Fetal Thymus	thymus

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