Variant report

Variant	rs7163986
Chromosome Location	chr15:42696158-42696159
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:42693940..42698488-chr15:42698720..42703314,5	K562	blood:

Variant related genes	Relation type
ENSG00000092529	Chromatin interaction

Extended variants
information (count: 88 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs1062038	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]
rs10775126	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs10851409	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs11070370	0.81[CEU][hapmap];1.00[CHB][hapmap];0.90[MEX][hapmap];0.84[YRI][hapmap]
rs1139100	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11631983	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs11638784	0.85[EUR][1000 genomes]
rs12101559	0.81[CHB][hapmap];0.90[CHD][hapmap];0.81[ASN][1000 genomes]
rs12438369	0.91[CEU][hapmap];0.85[MEX][hapmap];0.87[TSI][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12438453	0.91[CEU][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12438562	0.82[EUR][1000 genomes]
rs12441642	0.80[CEU][hapmap]
rs12441700	0.84[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];0.90[MEX][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12442040	0.81[ASN][1000 genomes]
rs12442046	0.81[ASN][1000 genomes]
rs1359003	0.84[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];0.90[MEX][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1359004	0.81[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes]
rs1659212	0.81[CEU][hapmap];1.00[CHB][hapmap];0.88[YRI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1659213	0.90[CHB][hapmap]
rs1659217	0.82[EUR][1000 genomes]
rs1659218	0.90[CHB][hapmap]
rs1659219	0.90[CHB][hapmap]
rs1659222	0.90[CHB][hapmap]
rs1678985	0.81[CEU][hapmap];0.91[CHB][hapmap]
rs1678986	0.81[CEU][hapmap];0.91[CHB][hapmap]
rs1678992	0.90[CHB][hapmap]
rs1678993	0.90[CHB][hapmap]
rs1679012	0.91[CHB][hapmap]
rs16973261	0.81[ASN][1000 genomes]
rs1703755	0.81[CEU][hapmap];0.91[CHB][hapmap]
rs1712418	0.81[CEU][hapmap];0.91[CHB][hapmap]
rs2289295	0.81[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes]
rs2407707	0.81[CEU][hapmap];0.86[EUR][1000 genomes]
rs2412705	0.82[EUR][1000 genomes]
rs28364388	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28364390	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28364416	0.86[EUR][1000 genomes]
rs2918459	0.81[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes]
rs2918460	0.90[CHB][hapmap];0.84[YRI][hapmap]
rs2918461	0.81[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes]
rs3742997	0.84[ASN][1000 genomes]
rs3743006	0.81[CEU][hapmap];1.00[CHB][hapmap];0.85[MEX][hapmap];0.82[EUR][1000 genomes]
rs3850774	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4329897	0.81[CEU][hapmap];1.00[CHB][hapmap];0.88[YRI][hapmap];0.82[EUR][1000 genomes]
rs4923940	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs4924645	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs4924653	1.00[CHB][hapmap]
rs4924658	0.80[CEU][hapmap];1.00[CHB][hapmap];0.84[YRI][hapmap]
rs4924674	0.81[CEU][hapmap];0.90[MEX][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4924676	0.91[ASN][1000 genomes]
rs56702977	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs57347762	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs57502147	0.91[ASN][1000 genomes]
rs57734638	0.81[ASN][1000 genomes]
rs60569090	0.81[ASN][1000 genomes]
rs61071861	0.89[ASN][1000 genomes]
rs61115119	0.81[ASN][1000 genomes]
rs6493027	0.81[CEU][hapmap];1.00[CHB][hapmap];0.83[YRI][hapmap]
rs6493045	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7166604	0.91[ASN][1000 genomes]
rs7166785	1.00[CHB][hapmap];0.88[YRI][hapmap];0.87[AMR][1000 genomes]
rs7168709	0.81[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7169521	0.91[ASN][1000 genomes]
rs7175863	0.82[EUR][1000 genomes]
rs7179709	0.90[CHB][hapmap]
rs7181688	0.81[ASN][1000 genomes]
rs7181742	0.81[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes]
rs7183015	0.80[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes]
rs7183546	0.81[CEU][hapmap];1.00[CHB][hapmap];0.85[MEX][hapmap];0.82[EUR][1000 genomes]
rs751572	0.91[CEU][hapmap];1.00[CHB][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs8024113	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8024732	0.81[CEU][hapmap];1.00[CHB][hapmap];0.90[MEX][hapmap];0.84[YRI][hapmap]
rs8025601	0.81[CEU][hapmap]
rs8026817	0.81[ASN][1000 genomes]
rs8027283	0.81[CHB][hapmap];0.81[ASN][1000 genomes]
rs8031315	0.81[CEU][hapmap];1.00[CHB][hapmap];0.90[MEX][hapmap];0.84[YRI][hapmap]
rs8036187	0.89[CEU][hapmap];0.91[CHB][hapmap]
rs8036380	0.82[EUR][1000 genomes]
rs8036596	0.81[CEU][hapmap];1.00[CHB][hapmap];0.90[MEX][hapmap];0.84[YRI][hapmap]
rs8037020	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs9920921	0.81[CEU][hapmap];1.00[CHB][hapmap];0.85[MEX][hapmap];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	nsv932995	chr15:42640015-42704121	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	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

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs7163986	MAP1A	cis	parietal	SCAN
rs7163986	SNAP23	cis	parietal	SCAN
rs7163986	WDR76	cis	cerebellum	SCAN
rs7163986	LRRC57	cis	multi-tissue	Pritchard
rs7163986	C15orf23	cis	parietal	SCAN
rs7163986	CDAN1	cis	parietal	SCAN
rs7163986	CAPN3	cis	parietal	SCAN

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42656800-42697800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr15:42675200-42702800	Weak transcription	Colon Smooth Muscle	Colon
3	chr15:42678600-42706800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr15:42678800-42702800	Weak transcription	NHLF	lung
5	chr15:42679000-42706800	Weak transcription	Right Atrium	heart
6	chr15:42680200-42696400	Weak transcription	HSMMtube	muscle
7	chr15:42683800-42704600	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr15:42689000-42697800	Weak transcription	NHEK	skin
9	chr15:42689000-42712400	Weak transcription	Fetal Brain Male	brain
10	chr15:42689400-42696800	Weak transcription	Psoas Muscle	Psoas
11	chr15:42689400-42703200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr15:42689800-42706600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr15:42690800-42702400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr15:42691000-42703000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr15:42691200-42696200	Strong transcription	Primary B cells from peripheral blood	blood
16	chr15:42691200-42696400	Strong transcription	Liver	Liver
17	chr15:42691200-42697000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
18	chr15:42691400-42696400	Strong transcription	Primary B cells from cord blood	blood
19	chr15:42691400-42696800	Strong transcription	Duodenum Mucosa	Duodenum
20	chr15:42691400-42697200	Strong transcription	Sigmoid Colon	Sigmoid Colon
21	chr15:42691600-42697400	Strong transcription	Stomach Smooth Muscle	stomach
22	chr15:42692400-42702400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr15:42692600-42702400	Weak transcription	Primary T helper cells fromperipheralblood	blood
24	chr15:42692600-42702400	Weak transcription	Aorta	Aorta
25	chr15:42692600-42708400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr15:42692800-42702800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr15:42693200-42697000	Strong transcription	Fetal Stomach	stomach
28	chr15:42693600-42697000	Strong transcription	Adipose Nuclei	Adipose
29	chr15:42693600-42697200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr15:42693600-42703000	Weak transcription	Brain Germinal Matrix	brain
31	chr15:42693800-42696400	Strong transcription	Rectal Mucosa Donor 29	rectum
32	chr15:42693800-42696600	Strong transcription	Ovary	ovary
33	chr15:42693800-42696600	Strong transcription	Placenta Amnion	Placenta Amnion
34	chr15:42693800-42696800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr15:42693800-42696800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr15:42693800-42697000	Strong transcription	Lung	lung
37	chr15:42693800-42697000	Strong transcription	Right Ventricle	heart
38	chr15:42693800-42697200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr15:42694000-42696600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr15:42694000-42696800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr15:42694000-42703000	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr15:42694200-42702400	Weak transcription	Placenta	Placenta
43	chr15:42694200-42704000	Weak transcription	Small Intestine	intestine
44	chr15:42694400-42696800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr15:42694600-42697400	Genic enhancers	Skeletal Muscle Male	skeletal muscle
46	chr15:42694600-42750600	Strong transcription	Primary neutrophils fromperipheralblood	blood
47	chr15:42694800-42696600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr15:42694800-42702200	Weak transcription	Thymus	Thymus
49	chr15:42694800-42702600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr15:42694800-42703000	Weak transcription	Primary hematopoietic stem cells	blood

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