Variant report

Variant	rs11164672
Chromosome Location	chr1:103571751-103571752
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	chr1:103571462..103572103-chr1:104003560..104004261,2	MCF-7	breast:

Extended variants
information (count: 120 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:117)

rs_ID	r²[population]
rs1012282	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10493986	0.83[CEU][hapmap]
rs10493988	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10493991	1.00[JPT][hapmap]
rs10747437	0.96[ASN][1000 genomes]
rs10782921	1.00[JPT][hapmap]
rs10874665	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10874668	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10874677	0.96[ASN][1000 genomes]
rs10874678	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10874679	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11164648	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11164649	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11164653	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11164657	0.84[ASN][1000 genomes]
rs11164658	1.00[JPT][hapmap]
rs11164662	0.88[CHB][hapmap];0.98[ASN][1000 genomes]
rs11164665	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11164666	0.84[EUR][1000 genomes]
rs11164667	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11164668	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11164669	0.96[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.87[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11586849	0.84[CEU][hapmap]
rs11809524	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11811018	1.00[JPT][hapmap]
rs12025848	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12036215	0.84[ASN][1000 genomes]
rs12042830	0.80[ASN][1000 genomes]
rs12047268	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12092111	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12118365	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12119459	1.00[JPT][hapmap]
rs12123031	1.00[JPT][hapmap]
rs12124588	1.00[JPT][hapmap]
rs12127590	1.00[JPT][hapmap]
rs12136338	1.00[JPT][hapmap]
rs12136748	1.00[JPT][hapmap]
rs12139120	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12142575	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12723167	1.00[JPT][hapmap]
rs12723922	1.00[JPT][hapmap]
rs12724152	1.00[JPT][hapmap]
rs12726958	1.00[JPT][hapmap]
rs12727959	1.00[JPT][hapmap]
rs12728397	1.00[JPT][hapmap]
rs12729449	1.00[JPT][hapmap]
rs12729602	1.00[JPT][hapmap]
rs12731843	1.00[JPT][hapmap]
rs12733933	1.00[JPT][hapmap]
rs12738133	1.00[JPT][hapmap]
rs12740738	0.98[ASN][1000 genomes]
rs12743365	1.00[JPT][hapmap]
rs12744290	1.00[JPT][hapmap]
rs12744488	1.00[JPT][hapmap]
rs12750377	1.00[JPT][hapmap]
rs12756627	1.00[JPT][hapmap]
rs1337174	1.00[JPT][hapmap]
rs1337175	1.00[JPT][hapmap]
rs1337186	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1337191	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1337195	0.83[CEU][hapmap]
rs1415359	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1415361	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1415364	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1463034	1.00[JPT][hapmap]
rs1463035	1.00[JPT][hapmap]
rs1538041	1.00[JPT][hapmap]
rs1564143	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1591636	1.00[JPT][hapmap]
rs1591637	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs17506286	1.00[JPT][hapmap]
rs17507967	1.00[JPT][hapmap]
rs1870958	1.00[JPT][hapmap]
rs1903787	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2050601	1.00[JPT][hapmap]
rs2061704	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2065922	0.89[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2252146	1.00[JPT][hapmap]
rs2254082	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2376280	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2376281	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2615977	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2615987	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2622848	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2622870	1.00[JPT][hapmap]
rs2622874	1.00[JPT][hapmap]
rs2622876	1.00[JPT][hapmap]
rs2622877	1.00[JPT][hapmap]
rs2622880	1.00[JPT][hapmap]
rs2786120	1.00[JPT][hapmap]
rs2786121	1.00[JPT][hapmap]
rs2786122	1.00[JPT][hapmap]
rs2786125	1.00[JPT][hapmap]
rs2889351	0.98[ASN][1000 genomes]
rs2929163	1.00[JPT][hapmap]
rs3102053	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3767272	0.82[JPT][hapmap]
rs3850459	1.00[JPT][hapmap]
rs3908854	0.84[ASN][1000 genomes]
rs4338381	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4391683	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4478834	1.00[JPT][hapmap]
rs4907986	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4908280	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4908286	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4908289	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4908291	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.92[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs6663034	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6670486	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6672647	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6695665	1.00[JPT][hapmap]
rs7517682	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7532572	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7544130	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7550118	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs945748	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs9970114	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][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	nsv522922	chr1:103305021-103764640	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv830893	chr1:103458498-103635579	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv931600	chr1:103548397-104161031	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:103567400-103575000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr1:103569400-103572600	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr1:103570200-103572200	Active TSS	Fetal Muscle Leg	muscle
4	chr1:103570400-103571800	Weak transcription	Fetal Heart	heart
5	chr1:103570400-103573400	Active TSS	Brain Germinal Matrix	brain
6	chr1:103570400-103575200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr1:103570600-103571800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr1:103570600-103571800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:103570600-103571800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr1:103570600-103571800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr1:103571400-103573600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr1:103571400-103574600	Active TSS	Cortex derived primary cultured neurospheres	brain
13	chr1:103571400-103574800	Active TSS	Fetal Brain Female	brain
14	chr1:103571600-103571800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr1:103571600-103572000	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
16	chr1:103571600-103572200	Active TSS	Osteobl	bone
17	chr1:103571600-103573000	Active TSS	HUES48 Cell Line	embryonic stem cell
18	chr1:103571600-103573200	Active TSS	NH-A	brain
19	chr1:103571600-103574600	Active TSS	HSMMtube	muscle

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