Variant report

Variant	rs12438369
Chromosome Location	chr15:42675034-42675035
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	chr15:42672860..42675186-chr15:42675250..42677559,2	K562	blood:
2	chr15:42453676..42456165-chr15:42673435..42675912,2	K562	blood:

Variant related genes	Relation type
ENSG00000166887	Chromatin interaction

Extended variants
information (count: 121 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:113)

rs_ID	r²[population]
rs10775126	0.90[CEU][hapmap];0.83[EUR][1000 genomes]
rs10851409	0.90[CEU][hapmap];0.83[EUR][1000 genomes]
rs11070370	0.90[CEU][hapmap];0.95[MEX][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes]
rs11631983	0.90[CEU][hapmap]
rs11638784	0.88[EUR][1000 genomes]
rs12438453	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12438509	1.00[ASW][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.89[LWK][hapmap];0.85[MEX][hapmap];0.88[MKK][hapmap];0.87[YRI][hapmap];0.84[ASN][1000 genomes]
rs12438562	0.85[EUR][1000 genomes]
rs12440087	0.85[CHB][hapmap];1.00[CHD][hapmap];0.84[ASN][1000 genomes]
rs12441642	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12441700	0.90[CEU][hapmap];0.95[MEX][hapmap];0.81[TSI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1359003	0.90[CEU][hapmap];0.95[MEX][hapmap];0.81[TSI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1359004	0.90[CEU][hapmap];0.88[EUR][1000 genomes]
rs1659212	0.90[CEU][hapmap];0.91[EUR][1000 genomes]
rs1659217	0.85[EUR][1000 genomes]
rs1678985	0.90[CEU][hapmap]
rs1678986	0.90[CEU][hapmap]
rs16972887	0.85[CHB][hapmap];0.84[ASN][1000 genomes]
rs16973008	1.00[ASW][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.96[LWK][hapmap];0.85[MEX][hapmap];0.91[MKK][hapmap];0.91[YRI][hapmap];0.84[ASN][1000 genomes]
rs16973045	0.85[CHB][hapmap];0.86[ASN][1000 genomes]
rs16973060	0.85[CHB][hapmap];0.89[ASN][1000 genomes]
rs1703750	0.90[CEU][hapmap]
rs1703755	0.90[CEU][hapmap]
rs1712418	0.90[CEU][hapmap]
rs2138831	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[MEX][hapmap]
rs2289295	0.90[CEU][hapmap];0.85[EUR][1000 genomes]
rs2407707	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2412688	0.85[CHB][hapmap];0.84[ASN][1000 genomes]
rs2412705	0.85[EUR][1000 genomes]
rs2412709	0.81[ASW][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs28364388	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28364390	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28364393	0.85[CHB][hapmap];1.00[CHD][hapmap];0.84[ASN][1000 genomes]
rs28364416	0.89[EUR][1000 genomes]
rs2918459	0.90[CEU][hapmap];0.85[EUR][1000 genomes]
rs2918461	0.90[CEU][hapmap];0.95[MEX][hapmap];0.81[TSI][hapmap];0.85[EUR][1000 genomes]
rs3742996	0.81[ASW][hapmap]
rs3743005	1.00[ASW][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];0.94[MKK][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs3743006	0.90[CEU][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.85[EUR][1000 genomes]
rs3743007	0.85[CHB][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs3743008	0.85[CHB][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs3825785	1.00[ASW][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];0.94[MKK][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs3850774	0.88[EUR][1000 genomes]
rs4329897	0.90[CEU][hapmap];0.85[EUR][1000 genomes]
rs4506867	0.85[CHB][hapmap];0.89[ASN][1000 genomes]
rs4923940	0.90[CEU][hapmap];0.83[EUR][1000 genomes]
rs4923943	0.83[EUR][1000 genomes]
rs4923945	0.82[CHB][hapmap];0.91[YRI][hapmap];0.89[ASN][1000 genomes]
rs4924630	0.85[CHB][hapmap]
rs4924644	0.84[ASN][1000 genomes]
rs4924645	0.90[CEU][hapmap]
rs4924653	0.86[CEU][hapmap]
rs4924658	0.89[CEU][hapmap];0.83[EUR][1000 genomes]
rs4924660	0.83[EUR][1000 genomes]
rs4924672	1.00[ASW][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.96[LWK][hapmap];0.85[MEX][hapmap];0.94[MKK][hapmap];0.91[YRI][hapmap];0.89[ASN][1000 genomes]
rs4924673	0.85[CHB][hapmap];0.91[YRI][hapmap];0.89[ASN][1000 genomes]
rs4924674	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.84[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4924675	1.00[JPT][hapmap]
rs55882551	0.84[ASN][1000 genomes]
rs56257215	0.84[ASN][1000 genomes]
rs56670003	0.84[ASN][1000 genomes]
rs56702977	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56987883	0.89[ASN][1000 genomes]
rs57002846	0.81[EUR][1000 genomes]
rs57134130	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs57347762	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs57933952	0.84[ASN][1000 genomes]
rs57973092	0.89[ASN][1000 genomes]
rs57976413	0.84[ASN][1000 genomes]
rs58292736	0.84[ASN][1000 genomes]
rs58313689	0.87[ASN][1000 genomes]
rs58712370	0.89[ASN][1000 genomes]
rs59094161	0.84[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs59132828	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59138723	0.84[ASN][1000 genomes]
rs59320762	0.89[ASN][1000 genomes]
rs59974698	0.84[ASN][1000 genomes]
rs60634548	0.84[ASN][1000 genomes]
rs61069354	0.84[ASN][1000 genomes]
rs61133768	0.84[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs6493027	0.90[CEU][hapmap]
rs6493033	0.84[ASN][1000 genomes]
rs6493045	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs677878	0.88[CEU][hapmap]
rs7163986	0.91[CEU][hapmap];0.85[MEX][hapmap];0.87[TSI][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7166785	0.80[CEU][hapmap];0.81[EUR][1000 genomes]
rs7168709	0.90[CEU][hapmap];0.89[EUR][1000 genomes]
rs7175863	0.85[EUR][1000 genomes]
rs7179203	0.88[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs7180279	1.00[ASW][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];0.94[MKK][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs7181742	0.90[CEU][hapmap];0.81[TSI][hapmap];0.85[EUR][1000 genomes]
rs7183015	0.89[CEU][hapmap];0.85[EUR][1000 genomes]
rs7183546	0.90[CEU][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.85[EUR][1000 genomes]
rs73398938	0.84[ASN][1000 genomes]
rs73400993	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73402707	0.83[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs73403365	0.84[ASN][1000 genomes]
rs73407488	0.84[ASN][1000 genomes]
rs73409577	0.81[ASN][1000 genomes]
rs751572	1.00[CEU][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs765830	0.81[EUR][1000 genomes]
rs8024113	0.81[CEU][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8024732	0.90[CEU][hapmap];0.95[MEX][hapmap];0.81[TSI][hapmap]
rs8025601	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8026198	0.81[EUR][1000 genomes]
rs8027016	0.84[ASN][1000 genomes]
rs8031315	0.90[CEU][hapmap];0.95[MEX][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes]
rs8036187	1.00[CEU][hapmap]
rs8036380	0.85[EUR][1000 genomes]
rs8036596	0.90[CEU][hapmap];0.95[MEX][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes]
rs8037020	0.90[CEU][hapmap];0.84[MEX][hapmap];0.81[TSI][hapmap]
rs8041951	0.89[ASN][1000 genomes]
rs9920921	0.90[CEU][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	nsv904133	chr15:42528982-42681057	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
5	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
6	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
7	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
8	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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs12438369	FRMD5	cis	cerebellum	SCAN
rs12438369	CDAN1	cis	parietal	SCAN
rs12438369	C15orf23	cis	parietal	SCAN
rs12438369	SNAP23	cis	parietal	SCAN
rs12438369	CAPN3	cis	parietal	SCAN
rs12438369	MAP1A	cis	parietal	SCAN
rs12438369	ZFP106	cis	lymphoblastoid	seeQTL
rs12438369	C15orf63	cis	parietal	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42645600-42677800	Weak transcription	Spleen	Spleen
2	chr15:42646000-42678600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr15:42647800-42678200	Weak transcription	Ovary	ovary
4	chr15:42652800-42684400	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr15:42653200-42691600	Weak transcription	Stomach Smooth Muscle	stomach
6	chr15:42654200-42677800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr15:42656000-42678800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr15:42656800-42693400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr15:42656800-42697800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr15:42657200-42678800	Weak transcription	Brain Cingulate Gyrus	brain
11	chr15:42659600-42676800	Weak transcription	Lung	lung
12	chr15:42663000-42691400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr15:42663200-42678400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr15:42666600-42676800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr15:42666600-42676800	Weak transcription	Fetal Muscle Leg	muscle
16	chr15:42666600-42676800	Weak transcription	Left Ventricle	heart
17	chr15:42666800-42676800	Weak transcription	Fetal Muscle Trunk	muscle
18	chr15:42670200-42676800	Weak transcription	Primary B cells from cord blood	blood
19	chr15:42670400-42676200	Weak transcription	Liver	Liver
20	chr15:42672200-42675200	Weak transcription	Primary monocytes fromperipheralblood	blood
21	chr15:42672400-42675200	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr15:42672400-42688800	Weak transcription	Esophagus	oesophagus
23	chr15:42672800-42675200	Weak transcription	Primary B cells from peripheral blood	blood
24	chr15:42673400-42691800	Weak transcription	Primary T cells from cord blood	blood
25	chr15:42673600-42675200	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr15:42673600-42676200	Weak transcription	Primary neutrophils fromperipheralblood	blood
27	chr15:42673800-42676800	Weak transcription	Brain Substantia Nigra	brain
28	chr15:42673800-42678000	Weak transcription	Fetal Intestine Small	intestine
29	chr15:42673800-42678200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr15:42674000-42694400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr15:42674200-42676400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr15:42674600-42678200	Weak transcription	Aorta	Aorta
33	chr15:42674600-42682600	Strong transcription	Monocytes-CD14+_RO01746	blood
34	chr15:42674600-42684400	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr15:42674800-42678400	Weak transcription	Brain Anterior Caudate	brain

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