Variant report

Variant	rs2171577
Chromosome Location	chr4:48388303-48388304
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	chr4:48342945..48345257-chr4:48386743..48389713,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000109171	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11932126	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1565218	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1565221	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17609521	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17609535	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17609556	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17609614	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17655725	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17655741	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4695378	0.86[EUR][1000 genomes]
rs55730515	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs55986500	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56932035	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57676508	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58038882	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58244627	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58707818	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60891069	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6810911	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6847014	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6852840	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs73814762	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73814763	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7693468	0.88[AMR][1000 genomes];0.91[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	nsv1006610	chr4:48209294-48415387	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv537085	chr4:48209294-48415387	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv528084	chr4:48387851-48413919	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48355000-48412600	Weak transcription	Aorta	Aorta
2	chr4:48355800-48390600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr4:48363400-48405400	Weak transcription	Right Ventricle	heart
4	chr4:48371400-48395400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr4:48372600-48426800	Weak transcription	Small Intestine	intestine
6	chr4:48377800-48405000	Weak transcription	Esophagus	oesophagus
7	chr4:48377800-48423800	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr4:48378000-48390000	Weak transcription	NHLF	lung
9	chr4:48378000-48423800	Weak transcription	Colon Smooth Muscle	Colon
10	chr4:48378200-48398400	Weak transcription	A549	lung
11	chr4:48378400-48395200	Weak transcription	Rectal Smooth Muscle	rectum
12	chr4:48378400-48405000	Weak transcription	Gastric	stomach
13	chr4:48378400-48405200	Weak transcription	Psoas Muscle	Psoas
14	chr4:48378600-48395200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr4:48379600-48391800	Strong transcription	Primary T helper cells PMA-I stimulated	--
16	chr4:48379600-48393600	Strong transcription	Primary T helper cells fromperipheralblood	blood
17	chr4:48379600-48400200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr4:48380000-48389200	Strong transcription	Fetal Lung	lung
19	chr4:48380000-48392000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr4:48380000-48399200	Strong transcription	Primary T cells fromperipheralblood	blood
21	chr4:48380200-48388600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr4:48381200-48389400	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr4:48381400-48405000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr4:48381600-48405000	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr4:48382000-48389000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr4:48382000-48389000	Strong transcription	Primary B cells from peripheral blood	blood
27	chr4:48382200-48398600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr4:48382200-48431800	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr4:48383000-48388400	Weak transcription	Brain Anterior Caudate	brain
30	chr4:48383000-48389200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr4:48383000-48397200	Strong transcription	Fetal Thymus	thymus
32	chr4:48383000-48398400	Weak transcription	Fetal Brain Female	brain
33	chr4:48383000-48405200	Weak transcription	Spleen	Spleen
34	chr4:48383200-48389400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr4:48383200-48390000	Weak transcription	Brain Substantia Nigra	brain
36	chr4:48383200-48390600	Weak transcription	Brain Cingulate Gyrus	brain
37	chr4:48383200-48397000	Weak transcription	HUVEC	blood vessel
38	chr4:48383200-48398800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
39	chr4:48383200-48412000	Weak transcription	Fetal Brain Male	brain
40	chr4:48383600-48389000	Strong transcription	HSMM	muscle
41	chr4:48383600-48398600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr4:48383800-48389400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr4:48383800-48390000	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr4:48383800-48395400	Weak transcription	HSMMtube	muscle
45	chr4:48383800-48397400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr4:48383800-48398000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr4:48384200-48388600	Strong transcription	Placenta	Placenta
48	chr4:48384200-48389200	Strong transcription	HUES64 Cell Line	embryonic stem cell
49	chr4:48384200-48403000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
50	chr4:48384400-48388400	Strong transcription	Breast Myoepithelial Primary Cells	Breast

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