Variant report

Variant	rs1062038
Chromosome Location	chr15:42707843-42707844
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:42698233..42703312-chr15:42703479..42708352,6	K562	blood:
2	chr15:42563602..42565878-chr15:42706468..42708668,2	MCF-7	breast:
3	chr15:42699538..42703312-chr15:42704209..42708483,5	K562	blood:

Variant related genes	Relation type
ENSG00000092529	Chromatin interaction
ENSG00000214013	Chromatin interaction
ENSG00000103978	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs1062015	0.82[ASN][1000 genomes]
rs10775126	0.81[CEU][hapmap];0.92[CHB][hapmap];0.81[EUR][1000 genomes]
rs10851409	0.81[CEU][hapmap];0.91[CHB][hapmap];0.81[EUR][1000 genomes]
rs11070370	0.91[CHB][hapmap];0.81[EUR][1000 genomes]
rs1139100	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11631983	0.81[CEU][hapmap];0.92[CHB][hapmap]
rs12101559	0.91[CHB][hapmap];0.90[ASN][1000 genomes]
rs12438562	0.83[EUR][1000 genomes]
rs12441700	0.91[CHB][hapmap];0.85[EUR][1000 genomes]
rs12442040	0.90[ASN][1000 genomes]
rs12442046	0.90[ASN][1000 genomes]
rs1359003	0.91[CHB][hapmap];0.85[EUR][1000 genomes]
rs1359004	0.81[CEU][hapmap];0.92[CHB][hapmap];0.85[EUR][1000 genomes]
rs1659212	0.81[CEU][hapmap];0.92[CHB][hapmap]
rs1659213	0.83[CHB][hapmap]
rs1659217	0.83[EUR][1000 genomes]
rs1659218	0.83[CHB][hapmap]
rs1659219	0.82[CHB][hapmap]
rs1659222	0.82[CHB][hapmap]
rs1678985	0.81[CEU][hapmap];0.84[CHB][hapmap]
rs1678986	0.82[CHB][hapmap]
rs1678992	0.83[CHB][hapmap]
rs1678993	0.83[CHB][hapmap]
rs1679012	0.82[CHB][hapmap]
rs16973261	0.90[ASN][1000 genomes]
rs16973265	0.80[YRI][hapmap]
rs1712418	0.81[CEU][hapmap];0.84[CHB][hapmap]
rs2289295	0.81[CEU][hapmap];0.92[CHB][hapmap];0.83[EUR][1000 genomes]
rs2407707	0.81[CEU][hapmap]
rs2412705	0.83[EUR][1000 genomes]
rs2918459	0.81[CEU][hapmap];0.92[CHB][hapmap];0.83[EUR][1000 genomes]
rs2918460	0.83[CHB][hapmap]
rs2918461	0.91[CHB][hapmap];0.83[EUR][1000 genomes]
rs3742997	0.88[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs3743006	0.91[CHB][hapmap];0.83[EUR][1000 genomes]
rs3850774	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4329897	0.81[CEU][hapmap];0.92[CHB][hapmap];0.83[EUR][1000 genomes]
rs4923940	0.81[CEU][hapmap];0.92[CHB][hapmap];0.81[EUR][1000 genomes]
rs4923943	0.81[EUR][1000 genomes]
rs4924645	0.81[CEU][hapmap];0.92[CHB][hapmap]
rs4924653	0.88[CEU][hapmap];0.92[CHB][hapmap]
rs4924658	0.92[CHB][hapmap];0.81[EUR][1000 genomes]
rs4924660	0.81[EUR][1000 genomes]
rs4924674	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4924676	1.00[ASN][1000 genomes]
rs57502147	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs57734638	0.90[ASN][1000 genomes]
rs60569090	0.90[ASN][1000 genomes]
rs61071861	0.99[ASN][1000 genomes]
rs61115119	0.90[ASN][1000 genomes]
rs6493027	0.81[CEU][hapmap];0.92[CHB][hapmap]
rs6493045	0.85[EUR][1000 genomes]
rs7163986	0.81[CEU][hapmap];0.91[CHB][hapmap];0.82[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7166604	1.00[ASN][1000 genomes]
rs7166785	0.92[CHB][hapmap];0.81[AMR][1000 genomes]
rs7168709	0.81[CEU][hapmap];0.92[CHB][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7169521	1.00[ASN][1000 genomes]
rs7175863	0.83[EUR][1000 genomes]
rs7179709	0.83[CHB][hapmap]
rs7181688	0.90[ASN][1000 genomes]
rs7181742	0.91[CHB][hapmap];0.83[EUR][1000 genomes]
rs7183015	0.90[CEU][hapmap];0.92[CHB][hapmap];0.83[EUR][1000 genomes]
rs7183546	0.91[CHB][hapmap];0.83[EUR][1000 genomes]
rs73400993	0.80[EUR][1000 genomes]
rs751572	0.91[CHB][hapmap];0.84[EUR][1000 genomes]
rs8024113	0.92[CHB][hapmap];0.82[JPT][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8024732	0.91[CHB][hapmap]
rs8025601	0.81[CEU][hapmap]
rs8026817	0.90[ASN][1000 genomes]
rs8027283	0.92[CHB][hapmap];0.90[ASN][1000 genomes]
rs8031315	0.91[CHB][hapmap];0.81[EUR][1000 genomes]
rs8036187	0.83[CHB][hapmap]
rs8036380	0.83[EUR][1000 genomes]
rs8036596	0.91[CHB][hapmap];0.81[EUR][1000 genomes]
rs8037020	0.91[CHB][hapmap]
rs9920921	0.91[CHB][hapmap];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931223	chr15:41989960-42781757	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
2	nsv1049445	chr15:42239738-42830484	Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
3	nsv542366	chr15:42239738-42830484	Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
4	nsv832986	chr15:42587825-42753664	Genic enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv832987	chr15:42627447-42792348	Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
6	esv3334708	chr15:42664344-42827738	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42689000-42712400	Weak transcription	Fetal Brain Male	brain
2	chr15:42692600-42708400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr15:42694600-42750600	Strong transcription	Primary neutrophils fromperipheralblood	blood
4	chr15:42694800-42708400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr15:42695000-42716000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr15:42697000-42708400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr15:42698400-42708400	Weak transcription	Fetal Kidney	kidney
8	chr15:42698600-42738400	Strong transcription	Fetal Muscle Leg	muscle
9	chr15:42699200-42741600	Strong transcription	Fetal Muscle Trunk	muscle
10	chr15:42700000-42732400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
11	chr15:42700200-42713600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr15:42700600-42710200	Strong transcription	Brain Anterior Caudate	brain
13	chr15:42700800-42708200	Weak transcription	Stomach Mucosa	stomach
14	chr15:42700800-42732000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr15:42700800-42747200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr15:42701000-42719200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr15:42701000-42738800	Strong transcription	Duodenum Smooth Muscle	Duodenum
18	chr15:42701200-42766600	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr15:42701400-42710200	Strong transcription	Brain Cingulate Gyrus	brain
20	chr15:42701400-42710200	Strong transcription	Brain Hippocampus Middle	brain
21	chr15:42701400-42710200	Strong transcription	Brain Substantia Nigra	brain
22	chr15:42701400-42732600	Strong transcription	Adipose Nuclei	Adipose
23	chr15:42701600-42744200	Strong transcription	Stomach Smooth Muscle	stomach
24	chr15:42701800-42732400	Strong transcription	Fetal Intestine Large	intestine
25	chr15:42702000-42711400	Strong transcription	Primary T cells from cord blood	blood
26	chr15:42702200-42719200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr15:42702200-42750200	Strong transcription	Primary monocytes fromperipheralblood	blood
28	chr15:42702400-42710200	Strong transcription	Primary B cells from cord blood	blood
29	chr15:42702400-42732600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr15:42702400-42744200	Strong transcription	Primary T helper cells fromperipheralblood	blood
31	chr15:42702400-42744200	Strong transcription	Liver	Liver
32	chr15:42702600-42708200	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr15:42702600-42708400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr15:42702600-42709800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr15:42702600-42713000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr15:42702600-42719400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr15:42702600-42724000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr15:42702600-42732400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr15:42702600-42738800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr15:42702600-42744400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr15:42702800-42708400	Weak transcription	Dnd41	blood
42	chr15:42702800-42711200	Strong transcription	Colon Smooth Muscle	Colon
43	chr15:42702800-42719200	Strong transcription	HSMMtube	muscle
44	chr15:42702800-42732000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr15:42702800-42744400	Strong transcription	Duodenum Mucosa	Duodenum
46	chr15:42703000-42708600	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr15:42703000-42710200	Strong transcription	Primary hematopoietic stem cells	blood
48	chr15:42703000-42710400	Strong transcription	HSMM	muscle
49	chr15:42703000-42726000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr15:42703000-42732200	Strong transcription	Primary hematopoietic stem cells short term culture	blood

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