Variant report

Variant	rs11749864
Chromosome Location	chr5:112612123-112612124
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	chr5:112611052..112612599-chr5:112628891..112631844,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000171444	Chromatin interaction

Extended variants
information (count: 116 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:112)

rs_ID	r²[population]
rs10077020	0.81[AMR][1000 genomes]
rs10428666	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10519343	1.00[CEU][hapmap];0.85[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10519345	0.85[JPT][hapmap];0.92[ASN][1000 genomes]
rs10519346	0.82[CEU][hapmap];0.85[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11241197	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11740045	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11740190	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11740233	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11740318	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11740353	1.00[CEU][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11740443	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11741794	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11741937	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11743052	0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs11744606	0.85[JPT][hapmap];0.95[ASN][1000 genomes]
rs11746532	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11746791	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11746821	0.92[ASN][1000 genomes]
rs11748058	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11748465	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11748503	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11748524	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12186466	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12188069	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12188070	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12188230	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12514091	0.85[CEU][hapmap];0.86[AMR][1000 genomes]
rs12518849	0.85[JPT][hapmap];0.92[ASN][1000 genomes]
rs12520003	1.00[CEU][hapmap]
rs12521391	0.82[CEU][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12522683	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12522862	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12523027	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12523255	0.82[JPT][hapmap]
rs12523284	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13360719	0.84[AMR][1000 genomes]
rs13436236	0.85[JPT][hapmap]
rs1443683	0.81[AMR][1000 genomes]
rs17135454	0.82[CEU][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17135463	0.82[CEU][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17135488	0.85[JPT][hapmap];0.92[ASN][1000 genomes]
rs17135506	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17135507	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17135514	1.00[CEU][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17135515	1.00[CEU][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17135517	1.00[CEU][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17135519	1.00[CEU][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17135520	1.00[CEU][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17135526	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17135531	1.00[CEU][hapmap];0.85[JPT][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17135534	0.85[JPT][hapmap];0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs17135535	1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17135542	0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs17135543	1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs17135546	1.00[CEU][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17164185	0.82[CEU][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1822488	0.85[JPT][hapmap]
rs1838208	0.82[AMR][1000 genomes]
rs1845289	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1850410	0.85[CEU][hapmap];0.97[EUR][1000 genomes]
rs1997521	0.90[ASN][1000 genomes]
rs2068923	0.81[AMR][1000 genomes]
rs2091803	0.85[ASN][1000 genomes]
rs2091804	0.85[ASN][1000 genomes]
rs34271294	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4632792	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4705549	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4705806	0.90[ASN][1000 genomes]
rs4705807	0.85[JPT][hapmap];0.92[ASN][1000 genomes]
rs4705808	0.92[ASN][1000 genomes]
rs4705809	0.85[JPT][hapmap];0.92[ASN][1000 genomes]
rs4705810	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4705811	0.86[ASN][1000 genomes]
rs4705817	0.85[JPT][hapmap]
rs56294433	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56362568	0.81[ASN][1000 genomes]
rs59107004	0.90[ASN][1000 genomes]
rs59222257	0.90[ASN][1000 genomes]
rs60087454	0.90[ASN][1000 genomes]
rs60437559	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62374372	0.82[AMR][1000 genomes]
rs6594695	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6594696	1.00[CEU][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6594697	1.00[CEU][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs66893265	0.90[ASN][1000 genomes]
rs67063423	0.90[ASN][1000 genomes]
rs67373655	0.90[ASN][1000 genomes]
rs67550282	0.90[ASN][1000 genomes]
rs68069850	0.90[ASN][1000 genomes]
rs6879761	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6887565	0.85[JPT][hapmap];0.95[ASN][1000 genomes]
rs6888602	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs73244759	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73244767	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73244770	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73244772	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73244779	0.90[ASN][1000 genomes]
rs73246604	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73246629	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73246648	0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs73246657	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs73246677	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73246681	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7703865	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7724707	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7724717	0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs7724936	0.85[JPT][hapmap];0.92[ASN][1000 genomes]
rs971370	1.00[JPT][hapmap];0.88[YRI][hapmap];0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs971371	1.00[JPT][hapmap];0.88[YRI][hapmap];0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs971373	1.00[JPT][hapmap];0.86[YRI][hapmap];0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs977997	1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv599396	chr5:112408944-112853189	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv882718	chr5:112519471-112674376	Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv882719	chr5:112568212-112706511	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv1024747	chr5:112592710-112679373	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112586600-112623600	Weak transcription	Pancreas	Pancrea
2	chr5:112587600-112617000	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr5:112600200-112618000	Weak transcription	Fetal Kidney	kidney
4	chr5:112601000-112612400	Enhancers	HUES48 Cell Line	embryonic stem cell
5	chr5:112602200-112616600	Weak transcription	Brain Hippocampus Middle	brain
6	chr5:112603000-112616800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr5:112603800-112612200	Enhancers	iPS-15b Cell Line	embryonic stem cell
8	chr5:112604400-112612600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr5:112604600-112612600	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr5:112605400-112612400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr5:112606600-112614000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr5:112607200-112614400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr5:112607600-112616200	Weak transcription	Esophagus	oesophagus
14	chr5:112608000-112628200	Weak transcription	HMEC	breast
15	chr5:112608200-112612200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr5:112608400-112612200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr5:112608600-112612400	Enhancers	ES-I3 Cell Line	embryonic stem cell
18	chr5:112608800-112612200	Enhancers	HUES6 Cell Line	embryonic stem cell
19	chr5:112609000-112612200	Enhancers	Ovary	ovary
20	chr5:112609200-112612400	Enhancers	Fetal Heart	heart
21	chr5:112609600-112612600	Enhancers	Left Ventricle	heart
22	chr5:112609600-112614800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr5:112610000-112628200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr5:112610400-112612200	Enhancers	H9 Cell Line	embryonic stem cell
25	chr5:112610600-112612200	Enhancers	Liver	Liver
26	chr5:112610800-112616400	Weak transcription	Spleen	Spleen
27	chr5:112610800-112623200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr5:112611000-112612400	Enhancers	Brain Cingulate Gyrus	brain
29	chr5:112611000-112614200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr5:112611000-112614200	Weak transcription	NH-A	brain
31	chr5:112611000-112614400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr5:112611000-112614800	Weak transcription	NHEK	skin
33	chr5:112611000-112616600	Weak transcription	Psoas Muscle	Psoas
34	chr5:112611000-112618000	Weak transcription	Fetal Stomach	stomach
35	chr5:112611000-112628200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr5:112611200-112612200	Enhancers	HUES64 Cell Line	embryonic stem cell
37	chr5:112611200-112612400	Enhancers	iPS-18 Cell Line	embryonic stem cell
38	chr5:112611200-112618000	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr5:112611400-112612400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr5:112611400-112614200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr5:112611400-112616400	Weak transcription	Adipose Nuclei	Adipose
42	chr5:112611400-112616400	Weak transcription	HUVEC	blood vessel
43	chr5:112611600-112612200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr5:112611800-112612400	Enhancers	iPS-20b Cell Line	embryonic stem cell
45	chr5:112611800-112612600	Enhancers	Brain Substantia Nigra	brain
46	chr5:112612000-112613600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr5:112612000-112613800	Weak transcription	Right Atrium	heart
48	chr5:112612000-112613800	Weak transcription	Right Ventricle	heart
49	chr5:112612000-112614400	Weak transcription	HSMMtube	muscle
50	chr5:112612000-112616400	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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