Variant report

Variant	rs11738060
Chromosome Location	chr5:180004154-180004155
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:180000027..180002613-chr5:180002639..180004210,2	MCF-7	breast:
2	chr5:180004083..180005642-chr5:180006961..180009387,2	MCF-7	breast:
3	chr5:180000649..180005755-chr5:180006610..180009607,4	K562	blood:
4	chr5:180000760..180002949-chr5:180003873..180005612,2	K562	blood:

Variant related genes	Relation type
ENSG00000263759	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs11249715	0.84[EUR][1000 genomes]
rs11249724	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11740121	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11740213	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11740953	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11741030	0.85[EUR][1000 genomes]
rs11742350	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11742375	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11744382	0.84[EUR][1000 genomes]
rs11744428	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11744582	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11745477	0.84[EUR][1000 genomes]
rs11745688	0.85[EUR][1000 genomes]
rs11748724	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11748792	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11750477	0.83[EUR][1000 genomes]
rs11949203	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11956078	0.85[EUR][1000 genomes]
rs11957507	0.84[EUR][1000 genomes]
rs11960298	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12109328	0.85[EUR][1000 genomes]
rs12110046	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12719870	0.83[EUR][1000 genomes]
rs13156947	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13171439	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13171609	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13171921	0.84[EUR][1000 genomes]
rs13174480	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13179742	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13181735	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13182919	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13183429	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13187624	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17630549	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17698422	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35076338	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35197594	0.85[EUR][1000 genomes]
rs35490561	0.83[EUR][1000 genomes]
rs56005965	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56039468	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs60034484	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62405525	0.86[EUR][1000 genomes]
rs62405531	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62405532	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62405547	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023914	chr5:179649883-180040672	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv537983	chr5:179649883-180040672	Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv1030697	chr5:179710469-180686563	ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	184 gene(s)	inside rSNPs	diseases
4	nsv1026417	chr5:179721376-180291360	Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
5	nsv1031836	chr5:179742033-180676122	Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	177 gene(s)	inside rSNPs	diseases
6	nsv537984	chr5:179742033-180676122	Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	177 gene(s)	inside rSNPs	diseases
7	nsv949199	chr5:179743553-180696889	Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	182 gene(s)	inside rSNPs	diseases
8	nsv830564	chr5:179867394-180010096	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
9	esv2762572	chr5:179996987-180183359	Bivalent Enhancer Strong transcription Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179970800-180006600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr5:179973800-180005200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr5:179974400-180005800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr5:179975000-180005800	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr5:179975600-180004600	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr5:179976200-180007200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr5:179985000-180005600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
8	chr5:179985400-180005800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr5:179987200-180005800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
10	chr5:179987400-180006000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr5:179987600-180005600	Strong transcription	HUES48 Cell Line	embryonic stem cell
12	chr5:179987800-180005200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr5:179988000-180005600	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr5:179988400-180005400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr5:179988400-180005800	Strong transcription	HUES6 Cell Line	embryonic stem cell
16	chr5:179988400-180005800	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chr5:179988400-180005800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr5:179988600-180004600	Strong transcription	H1 Cell Line	embryonic stem cell
19	chr5:179988600-180005200	Strong transcription	Primary B cells from peripheral blood	blood
20	chr5:179988800-180005400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr5:179988800-180005800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
22	chr5:179990600-180004600	Strong transcription	Duodenum Smooth Muscle	Duodenum
23	chr5:179990600-180005600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr5:179990800-180005400	Strong transcription	Primary T helper cells fromperipheralblood	blood
25	chr5:179991000-180005400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr5:179991000-180005800	Strong transcription	Primary B cells from cord blood	blood
27	chr5:179991000-180005800	Strong transcription	Duodenum Mucosa	Duodenum
28	chr5:179991000-180005800	Strong transcription	Fetal Intestine Large	intestine
29	chr5:179991000-180006400	Strong transcription	Primary neutrophils fromperipheralblood	blood
30	chr5:179991200-180005000	Weak transcription	Brain Cingulate Gyrus	brain
31	chr5:179991200-180005400	Weak transcription	Stomach Mucosa	stomach
32	chr5:179991200-180005600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr5:179991200-180005800	Strong transcription	Dnd41	blood
34	chr5:179991200-180005800	Strong transcription	GM12878-XiMat	blood
35	chr5:179991400-180004600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr5:179991400-180005600	Strong transcription	Liver	Liver
37	chr5:179991600-180005800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr5:179991600-180005800	Strong transcription	Fetal Thymus	thymus
39	chr5:179991600-180006400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
40	chr5:179991800-180005800	Strong transcription	Placenta	Placenta
41	chr5:179992000-180004800	Strong transcription	Fetal Muscle Leg	muscle
42	chr5:179992000-180004800	Strong transcription	Sigmoid Colon	Sigmoid Colon
43	chr5:179992200-180004800	Strong transcription	Fetal Lung	lung
44	chr5:179992400-180006000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr5:179993200-180007600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
46	chr5:179993400-180005400	Weak transcription	Small Intestine	intestine
47	chr5:179993400-180005600	Weak transcription	Rectal Smooth Muscle	rectum
48	chr5:179993400-180007200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
49	chr5:179993400-180008000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr5:179994200-180004600	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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