Variant report

Variant	rs4329897
Chromosome Location	chr15:42649924-42649925
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:42649476-42650942	K562	blood:	n/a	n/a

Variant related genes	Relation type
CAPN3	TF binding region

Extended variants
information (count: 109 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:102)

rs_ID	r²[population]
rs1062038	0.81[CEU][hapmap];0.92[CHB][hapmap];0.83[EUR][1000 genomes]
rs10775126	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10851407	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10851408	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10851409	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11070370	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1139100	0.83[EUR][1000 genomes]
rs11631917	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11631983	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11638784	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12101559	0.81[CHB][hapmap]
rs12438369	0.90[CEU][hapmap];0.85[EUR][1000 genomes]
rs12438453	0.91[CEU][hapmap]
rs12438562	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12441642	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs12441700	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12594162	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12917101	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1359003	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1359004	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1619030	1.00[CEU][hapmap];0.91[CHB][hapmap];0.83[EUR][1000 genomes]
rs1659212	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1659213	0.91[CHB][hapmap];0.88[JPT][hapmap];0.94[ASN][1000 genomes]
rs1659217	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1659218	0.91[CHB][hapmap];0.88[JPT][hapmap];0.94[ASN][1000 genomes]
rs1659219	0.90[CHB][hapmap];0.88[JPT][hapmap];0.81[YRI][hapmap];0.94[ASN][1000 genomes]
rs1659221	0.94[ASN][1000 genomes]
rs1659222	0.90[CHB][hapmap];0.88[JPT][hapmap];0.94[ASN][1000 genomes]
rs1678984	0.94[ASN][1000 genomes]
rs1678985	1.00[CEU][hapmap];0.92[CHB][hapmap];0.83[EUR][1000 genomes]
rs1678986	1.00[CEU][hapmap];0.91[CHB][hapmap];0.82[EUR][1000 genomes]
rs1678991	0.84[EUR][1000 genomes]
rs1678992	0.91[CHB][hapmap];0.92[ASN][1000 genomes]
rs1678993	0.91[CHB][hapmap];0.92[ASN][1000 genomes]
rs1679002	0.85[EUR][1000 genomes]
rs1679009	1.00[CEU][hapmap];0.91[CHB][hapmap];0.83[EUR][1000 genomes]
rs1679010	1.00[CEU][hapmap];0.91[CHB][hapmap];0.83[EUR][1000 genomes]
rs1679012	0.91[CHB][hapmap]
rs1703750	1.00[CEU][hapmap];0.92[CHB][hapmap];0.85[EUR][1000 genomes]
rs1703755	0.91[CEU][hapmap];0.92[CHB][hapmap];0.82[EUR][1000 genomes]
rs1712418	1.00[CEU][hapmap];0.92[CHB][hapmap];0.84[EUR][1000 genomes]
rs1712421	0.84[EUR][1000 genomes]
rs2138831	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs2289295	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2407707	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs2412682	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2412685	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2412705	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28364388	0.86[EUR][1000 genomes]
rs28364390	0.85[EUR][1000 genomes]
rs28364416	0.89[JPT][hapmap];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2918459	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2918460	0.91[CHB][hapmap];0.88[JPT][hapmap];0.92[YRI][hapmap];0.94[ASN][1000 genomes]
rs2918461	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3743006	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3850774	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4923940	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4923943	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4924645	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4924648	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4924653	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4924658	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4924660	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4924674	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56702977	0.86[EUR][1000 genomes]
rs57002846	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs57347762	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58313689	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs59132828	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs598360	0.85[EUR][1000 genomes]
rs622442	1.00[CEU][hapmap];0.91[CHB][hapmap];0.83[EUR][1000 genomes]
rs633934	1.00[CEU][hapmap];0.92[CHB][hapmap];0.83[EUR][1000 genomes]
rs6493027	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6493045	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs660126	1.00[CEU][hapmap];0.92[CHB][hapmap];0.87[EUR][1000 genomes]
rs677878	1.00[CEU][hapmap];0.90[CHB][hapmap];0.82[EUR][1000 genomes]
rs7086	1.00[CEU][hapmap];0.92[CHB][hapmap]
rs7163986	0.81[CEU][hapmap];1.00[CHB][hapmap];0.88[YRI][hapmap];0.82[EUR][1000 genomes]
rs7166785	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7168709	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7175863	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7177120	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7179709	0.91[CHB][hapmap];0.88[JPT][hapmap]
rs7181742	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7183015	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7183546	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73400993	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs751572	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs765830	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8024113	1.00[CHB][hapmap]
rs8024732	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8025601	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8026198	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8027283	0.83[CHB][hapmap]
rs8031315	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8036046	0.87[EUR][1000 genomes]
rs8036187	1.00[CEU][hapmap];0.92[CHB][hapmap];0.87[EUR][1000 genomes]
rs8036380	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8036596	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8037020	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9672382	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9920921	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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	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

No data

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42568400-42656000	Weak transcription	Small Intestine	intestine
2	chr15:42604600-42651200	Weak transcription	Fetal Kidney	kidney
3	chr15:42619600-42656200	Weak transcription	HMEC	breast
4	chr15:42627600-42654600	Weak transcription	HSMM	muscle
5	chr15:42630600-42650600	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr15:42631800-42651000	Weak transcription	Fetal Heart	heart
7	chr15:42632200-42652600	Strong transcription	Primary B cells from peripheral blood	blood
8	chr15:42634600-42650400	Strong transcription	Rectal Mucosa Donor 29	rectum
9	chr15:42636400-42656600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr15:42637200-42653600	Weak transcription	Brain Germinal Matrix	brain
11	chr15:42638400-42651800	Weak transcription	Psoas Muscle	Psoas
12	chr15:42639400-42658600	Weak transcription	Hela-S3	cervix
13	chr15:42639800-42652200	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr15:42641400-42657400	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr15:42641800-42652800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr15:42642400-42655400	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr15:42643000-42650400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr15:42643000-42650800	Strong transcription	Adipose Nuclei	Adipose
19	chr15:42643000-42654800	Strong transcription	Liver	Liver
20	chr15:42643200-42650800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr15:42645000-42652400	Weak transcription	Rectal Smooth Muscle	rectum
22	chr15:42645000-42656600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr15:42645000-42656800	Weak transcription	Brain Cingulate Gyrus	brain
24	chr15:42645600-42650000	Weak transcription	Gastric	stomach
25	chr15:42645600-42654400	Weak transcription	NHLF	lung
26	chr15:42645600-42655000	Weak transcription	Right Ventricle	heart
27	chr15:42645600-42655200	Weak transcription	Pancreas	Pancrea
28	chr15:42645600-42663000	Weak transcription	NHDF-Ad	bronchial
29	chr15:42645600-42663600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr15:42645600-42677800	Weak transcription	Spleen	Spleen
31	chr15:42645800-42652000	Weak transcription	Fetal Stomach	stomach
32	chr15:42645800-42653200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr15:42645800-42653200	Weak transcription	Fetal Lung	lung
34	chr15:42646000-42652000	Weak transcription	Brain Hippocampus Middle	brain
35	chr15:42646000-42654000	Weak transcription	Colon Smooth Muscle	Colon
36	chr15:42646000-42654600	Weak transcription	GM12878-XiMat	blood
37	chr15:42646000-42654800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr15:42646000-42655400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr15:42646000-42656200	Weak transcription	NHEK	skin
40	chr15:42646000-42662600	Weak transcription	Brain Substantia Nigra	brain
41	chr15:42646000-42678600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr15:42646200-42650400	Weak transcription	Fetal Muscle Trunk	muscle
43	chr15:42646200-42651000	Weak transcription	Primary neutrophils fromperipheralblood	blood
44	chr15:42646400-42654800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr15:42646600-42656000	Weak transcription	Colonic Mucosa	Colon
46	chr15:42646800-42650200	Genic enhancers	Fetal Muscle Leg	muscle
47	chr15:42647000-42651200	Strong transcription	Primary T cells from cord blood	blood
48	chr15:42647200-42650200	Enhancers	Skeletal Muscle Female	skeletal muscle
49	chr15:42647200-42653600	Weak transcription	Primary T helper cells PMA-I stimulated	--
50	chr15:42647200-42656600	Weak transcription	Brain Angular Gyrus	brain

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