Variant report

Variant	rs13140943
Chromosome Location	chr4:6977109-6977110
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:6975991..6978450-chr4:6986422..6990391,3	MCF-7	breast:
2	chr4:6918088..6920742-chr4:6973003..6977658,4	MCF-7	breast:
3	chr4:6970136..6972569-chr4:6974039..6977282,3	MCF-7	breast:
4	chr4:6964971..6966612-chr4:6976027..6977681,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000132405	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10009332	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10013211	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10013696	0.99[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10015163	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10022869	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10155208	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10937771	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11723686	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12512922	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12648134	0.83[AMR][1000 genomes]
rs12650200	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12650264	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs17742611	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17743234	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2301820	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2301821	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28380685	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34173965	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35490604	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35772786	0.81[AMR][1000 genomes]
rs3857168	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3857169	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3857170	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3892145	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3892976	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4234790	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4315786	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4346651	0.81[ASN][1000 genomes]
rs4484301	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4689571	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4689572	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs56307635	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs58935653	0.81[ASN][1000 genomes]
rs6834007	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6852468	0.81[EUR][1000 genomes]
rs7672632	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9790586	0.81[ASN][1000 genomes]
rs9999127	0.85[AMR][1000 genomes];0.89[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	nsv878529	chr4:6883012-6983677	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv878530	chr4:6888932-7058473	Strong transcription Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	esv34033	chr4:6973270-7390621	Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:6965400-6987800	Weak transcription	Small Intestine	intestine
2	chr4:6968000-6987600	Weak transcription	HSMM	muscle
3	chr4:6969800-6985200	Weak transcription	Primary hematopoietic stem cells	blood
4	chr4:6969800-6986000	Weak transcription	Left Ventricle	heart
5	chr4:6970800-6985800	Weak transcription	Esophagus	oesophagus
6	chr4:6970800-6987800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr4:6971600-6986400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr4:6972000-6986000	Weak transcription	Right Ventricle	heart
9	chr4:6972400-6985800	Weak transcription	Duodenum Mucosa	Duodenum
10	chr4:6972400-6986000	Weak transcription	Ovary	ovary
11	chr4:6972800-6985800	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr4:6973800-6985000	Weak transcription	Spleen	Spleen
13	chr4:6974000-6985400	Weak transcription	HepG2	liver
14	chr4:6974800-6985800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr4:6975200-6978000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr4:6975200-6985600	Weak transcription	Fetal Intestine Small	intestine
17	chr4:6976000-6977400	Enhancers	Primary T helper naive cells from peripheral blood	blood
18	chr4:6976200-6978200	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr4:6976200-6978400	Weak transcription	Fetal Intestine Large	intestine
20	chr4:6976200-6985200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr4:6976200-6985200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr4:6976200-6985200	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr4:6976200-6985800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr4:6976200-6987800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr4:6976400-6978200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr4:6976400-6980800	Weak transcription	Stomach Mucosa	stomach
27	chr4:6976400-6985000	Weak transcription	Primary monocytes fromperipheralblood	blood
28	chr4:6976400-6985600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr4:6976400-6985800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr4:6976400-6986000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr4:6976400-6986000	Weak transcription	Placenta	Placenta
32	chr4:6976400-6987800	Weak transcription	Fetal Thymus	thymus
33	chr4:6976600-6978000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr4:6976600-6978000	Weak transcription	Brain Substantia Nigra	brain
35	chr4:6976600-6978400	Weak transcription	K562	blood
36	chr4:6976600-6980600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr4:6976600-6983200	Weak transcription	Monocytes-CD14+_RO01746	blood
38	chr4:6976600-6983400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr4:6976600-6985000	Weak transcription	Primary neutrophils fromperipheralblood	blood
40	chr4:6976600-6985000	Weak transcription	Primary B cells from cord blood	blood
41	chr4:6976600-6985400	Weak transcription	Primary T helper cells PMA-I stimulated	--
42	chr4:6976600-6985400	Weak transcription	Brain Hippocampus Middle	brain
43	chr4:6976600-6985800	Weak transcription	Primary T cells from cord blood	blood
44	chr4:6976600-6985800	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr4:6976600-6986000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr4:6976600-6986000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr4:6976600-6986000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr4:6976600-6986000	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr4:6976600-6986400	Weak transcription	A549	lung
50	chr4:6976600-6987000	Weak transcription	Fetal Kidney	kidney

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