Variant report

Variant	rs1496600
Chromosome Location	chr4:79389651-79389652
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	chr4:79384669..79386505-chr4:79388751..79390880,2	MCF-7	breast:

Extended variants
information (count: 118 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:116)

rs_ID	r²[population]
rs10023714	0.88[EUR][1000 genomes]
rs10518200	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11098197	0.89[EUR][1000 genomes]
rs11098208	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11721380	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11722061	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11723383	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11723415	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11724180	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11725388	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11727119	1.00[ASN][1000 genomes]
rs11727137	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11728117	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11728640	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11728758	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11728817	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11729604	0.84[AFR][1000 genomes]
rs11729705	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11730601	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11730636	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11730668	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11731012	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11731074	0.88[EUR][1000 genomes]
rs11731315	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11731480	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11733290	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11733471	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11736504	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11932879	1.00[ASN][1000 genomes]
rs11933879	1.00[ASN][1000 genomes]
rs11937000	1.00[ASN][1000 genomes]
rs11937001	1.00[ASN][1000 genomes]
rs11939230	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11939289	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11940228	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11941299	0.89[EUR][1000 genomes]
rs11943426	0.84[AFR][1000 genomes]
rs13101600	0.89[EUR][1000 genomes]
rs1353527	0.89[EUR][1000 genomes]
rs1390742	1.00[ASN][1000 genomes]
rs1496603	0.89[EUR][1000 genomes]
rs1496604	0.89[EUR][1000 genomes]
rs17003235	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17427362	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17429053	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17429432	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17429467	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17429649	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17429670	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17429718	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17429816	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17429963	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17430075	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17430137	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17430229	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17430243	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17430334	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17469341	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17469981	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17470002	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17470023	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17470072	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17470303	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17470490	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17470553	1.00[ASN][1000 genomes]
rs17470609	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17470811	1.00[ASN][1000 genomes]
rs17471069	1.00[ASN][1000 genomes]
rs17471104	1.00[ASN][1000 genomes]
rs17471139	1.00[ASN][1000 genomes]
rs17481799	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1826845	0.89[EUR][1000 genomes]
rs28568377	0.89[EUR][1000 genomes]
rs28694126	0.87[EUR][1000 genomes]
rs34435856	0.88[EUR][1000 genomes]
rs34678339	0.82[AFR][1000 genomes]
rs34806279	0.82[AFR][1000 genomes]
rs35933858	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4416499	0.88[EUR][1000 genomes]
rs4975129	0.86[EUR][1000 genomes]
rs4975130	0.87[EUR][1000 genomes]
rs55849455	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56681862	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56874454	1.00[ASN][1000 genomes]
rs57325795	1.00[ASN][1000 genomes]
rs57356999	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs57558056	1.00[ASN][1000 genomes]
rs57771713	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs58467919	1.00[ASN][1000 genomes]
rs58547899	1.00[ASN][1000 genomes]
rs59347621	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59373877	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59658562	0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs60144489	0.89[EUR][1000 genomes]
rs60253739	0.88[EUR][1000 genomes]
rs60805155	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs60991776	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs61185935	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs61346341	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6817408	0.89[EUR][1000 genomes]
rs6819837	0.87[EUR][1000 genomes]
rs6825278	0.88[EUR][1000 genomes]
rs6827590	0.87[EUR][1000 genomes]
rs6846802	0.89[EUR][1000 genomes]
rs6850657	0.89[EUR][1000 genomes]
rs72659058	1.00[ASN][1000 genomes]
rs72873310	1.00[ASN][1000 genomes]
rs72873312	1.00[ASN][1000 genomes]
rs72873313	1.00[ASN][1000 genomes]
rs7436657	0.89[EUR][1000 genomes]
rs7660569	0.89[EUR][1000 genomes]
rs7675866	1.00[ASN][1000 genomes]
rs7686157	0.89[EUR][1000 genomes]
rs931603	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs931605	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs931607	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534024	chr4:78785189-79437403	ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv1009633	chr4:78887573-79652236	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:79320000-79400200	Weak transcription	Psoas Muscle	Psoas
2	chr4:79333200-79391000	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr4:79343200-79431800	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr4:79354000-79391000	Weak transcription	Left Ventricle	heart
5	chr4:79354000-79401600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr4:79354200-79391000	Weak transcription	Fetal Kidney	kidney
7	chr4:79363200-79409800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr4:79363400-79455200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr4:79363800-79464200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr4:79365600-79406400	Strong transcription	HUES48 Cell Line	embryonic stem cell
11	chr4:79366200-79408200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
12	chr4:79369400-79397800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr4:79372600-79395000	Weak transcription	Stomach Smooth Muscle	stomach
14	chr4:79374000-79397600	Weak transcription	Fetal Lung	lung
15	chr4:79374200-79398800	Weak transcription	Esophagus	oesophagus
16	chr4:79374600-79391000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr4:79375800-79391000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr4:79376200-79390000	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr4:79376200-79398600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr4:79376200-79411600	Weak transcription	Fetal Stomach	stomach
21	chr4:79377000-79396200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr4:79378600-79455800	Weak transcription	Right Ventricle	heart
23	chr4:79378800-79395800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr4:79379800-79393200	Weak transcription	Brain Anterior Caudate	brain
25	chr4:79383600-79389800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr4:79384600-79395600	Strong transcription	HUES6 Cell Line	embryonic stem cell
27	chr4:79384600-79396600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr4:79384600-79405400	Strong transcription	H1 Cell Line	embryonic stem cell
29	chr4:79384800-79405000	Strong transcription	HUES64 Cell Line	embryonic stem cell
30	chr4:79384800-79405600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
31	chr4:79385000-79467400	Weak transcription	Fetal Brain Male	brain
32	chr4:79385800-79396600	Weak transcription	Pancreas	Pancrea
33	chr4:79385800-79398800	Weak transcription	Aorta	Aorta
34	chr4:79386000-79391800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr4:79387000-79390000	Weak transcription	Fetal Heart	heart
36	chr4:79387600-79391000	Weak transcription	Fetal Intestine Small	intestine
37	chr4:79387600-79391200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr4:79387800-79389800	Weak transcription	HSMMtube	muscle
39	chr4:79387800-79390800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr4:79387800-79391000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
41	chr4:79387800-79391000	Weak transcription	HepG2	liver
42	chr4:79387800-79396000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr4:79388200-79405000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
44	chr4:79388600-79397600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr4:79388800-79392000	Weak transcription	Fetal Muscle Leg	muscle
46	chr4:79389600-79393600	Strong transcription	Fetal Intestine Large	intestine
47	chr4:79389600-79393800	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr4:79389600-79395000	Strong transcription	H9 Cell Line	embryonic stem cell

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