Variant report

Variant	rs2470134
Chromosome Location	chr15:43849886-43849887
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 111 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs10163054	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs10438303	0.88[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs10518820	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11070408	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs11856184	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12441127	0.88[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap]
rs12443102	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes]
rs16950562	0.88[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs1814538	0.88[CEU][hapmap]
rs2245715	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2251844	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2253708	0.88[CEU][hapmap]
rs2255042	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2255051	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2255440	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2260160	1.00[CEU][hapmap]
rs2278860	0.88[CEU][hapmap]
rs2412779	0.88[CEU][hapmap]
rs2412780	0.88[CEU][hapmap]
rs2439	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2439831	0.88[CEU][hapmap]
rs2439832	1.00[CEU][hapmap]
rs2439834	0.81[AMR][1000 genomes]
rs2439850	0.87[CEU][hapmap]
rs2444032	0.88[CEU][hapmap]
rs2444250	0.88[CEU][hapmap]
rs2447193	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes]
rs2447196	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2447197	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2447198	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2447208	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes]
rs2447211	1.00[CEU][hapmap];0.82[AMR][1000 genomes]
rs2447212	0.82[AMR][1000 genomes]
rs2447213	0.81[AMR][1000 genomes]
rs2467402	0.86[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap]
rs2467426	1.00[CEU][hapmap]
rs2467736	0.88[CEU][hapmap]
rs2467739	0.88[CEU][hapmap]
rs2467746	0.82[EUR][1000 genomes]
rs2470120	0.80[ASN][1000 genomes]
rs2470121	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes]
rs2470130	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2470131	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2614811	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs2614819	1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2614822	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28366727	0.82[ASN][1000 genomes]
rs28475234	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28495368	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs28606452	0.83[AMR][1000 genomes]
rs2899082	0.88[CEU][hapmap]
rs2915776	0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2915779	0.83[AMR][1000 genomes]
rs2915788	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2915792	0.85[AMR][1000 genomes]
rs2920780	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2920781	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs2927071	0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2927072	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2927075	0.80[AMR][1000 genomes]
rs2957637	0.84[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2957639	0.82[ASN][1000 genomes]
rs3097773	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3099045	0.80[ASN][1000 genomes]
rs3101443	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs3809481	0.88[CEU][hapmap];0.90[CHB][hapmap]
rs4075674	0.88[CEU][hapmap]
rs475486	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs486301	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs495175	0.88[CEU][hapmap]
rs496584	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4997480	0.88[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs527921	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs544122	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs56397895	0.84[AMR][1000 genomes]
rs57865312	0.85[AMR][1000 genomes]
rs689647	0.88[CEU][hapmap]
rs689754	0.87[CEU][hapmap]
rs689781	0.88[CEU][hapmap]
rs689826	0.88[CEU][hapmap]
rs689835	0.88[CEU][hapmap]
rs689883	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs690170	0.85[ASN][1000 genomes]
rs690316	0.88[CEU][hapmap]
rs690436	0.88[CEU][hapmap]
rs694985	0.88[CEU][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7171750	0.88[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap]
rs7173487	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs7175129	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs8033995	0.88[CEU][hapmap]
rs8042868	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534649	chr15:43591116-43851142	Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	esv1846172	chr15:43632138-44116986	Bivalent Enhancer Weak transcription Genic enhancers Strong transcription Active TSS Enhancers Flanking Active TSS 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	101 gene(s)	inside rSNPs	diseases
3	esv1846701	chr15:43759774-44116986	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
4	nsv437799	chr15:43784000-43989518	Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	nsv832988	chr15:43804641-43976862	Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Genic enhancers Active TSS Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
6	nsv428304	chr15:43823158-44008580	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
7	esv2758379	chr15:43823158-44148641	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
8	esv2760028	chr15:43823158-44148641	Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
9	nsv427960	chr15:43823158-44148641	Flanking Active TSS Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
10	nsv428633	chr15:43823160-44008580	Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
11	nsv1039949	chr15:43831879-43992646	Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
12	esv2757598	chr15:43831923-44058634	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
13	esv2761766	chr15:43834318-44014255	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
14	nsv524910	chr15:43836478-43939642	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
15	nsv904148	chr15:43836478-43961204	Weak transcription Strong transcription ZNF genes & repeats Enhancers Bivalent Enhancer Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
16	nsv904149	chr15:43836478-44011113	Weak transcription Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
17	nsv904150	chr15:43836478-44040965	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
18	nsv1039818	chr15:43845410-43988541	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
19	nsv1048041	chr15:43845410-43991014	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
20	esv2760393	chr15:43845422-44024490	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs2470134	CKMT1A	cis	Esophagus Mucosa	GTEx
rs2470134	ADAL	cis	Esophagus Muscularis	GTEx
rs2470134	ADAL	cis	lung	GTEx
rs2470134	ADAL	cis	Artery Aorta	GTEx
rs2470134	ADAL	cis	Thyroid	GTEx
rs2470134	ADAL	cis	Artery Tibial	GTEx
rs2470134	ELL3	cis	multi-tissue	Pritchard
rs2470134	ADAL	cis	Skin Sun Exposed Lower leg	GTEx
rs2470134	ELL3	Cis_1M	lymphoblastoid	RTeQTL
rs2470134	ADAL	cis	Adipose Subcutaneous	GTEx
rs2470134	CATSPER2	cis	Esophagus Mucosa	GTEx
rs2470134	ADAL	cis	Nerve Tibial	GTEx
rs2470134	AC011330.5	cis	Esophagus Mucosa	GTEx

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:43818000-43852600	Weak transcription	Rectal Smooth Muscle	rectum
2	chr15:43818200-43851600	Weak transcription	Primary hematopoietic stem cells	blood
3	chr15:43823800-43852600	Weak transcription	Primary monocytes fromperipheralblood	blood
4	chr15:43824800-43853000	Weak transcription	GM12878-XiMat	blood
5	chr15:43824800-43853200	Weak transcription	Hela-S3	cervix
6	chr15:43827400-43852600	Weak transcription	Left Ventricle	heart
7	chr15:43827400-43854000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr15:43827600-43851200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr15:43827600-43851400	Weak transcription	Right Ventricle	heart
10	chr15:43827600-43851800	Weak transcription	Primary B cells from peripheral blood	blood
11	chr15:43827600-43852800	Weak transcription	Lung	lung
12	chr15:43827600-43854000	Weak transcription	Aorta	Aorta
13	chr15:43827600-43855400	Weak transcription	Ovary	ovary
14	chr15:43827800-43850000	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr15:43827800-43850400	Weak transcription	Primary B cells from cord blood	blood
16	chr15:43827800-43850800	Weak transcription	Esophagus	oesophagus
17	chr15:43827800-43851600	Weak transcription	Thymus	Thymus
18	chr15:43827800-43852800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr15:43828000-43851400	Weak transcription	Primary T cells fromperipheralblood	blood
20	chr15:43829000-43850400	Weak transcription	Monocytes-CD14+_RO01746	blood
21	chr15:43829000-43852600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr15:43837000-43851200	Strong transcription	Fetal Intestine Small	intestine
23	chr15:43837200-43851400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr15:43839800-43853000	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr15:43840200-43852600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr15:43840200-43853200	Weak transcription	HMEC	breast
27	chr15:43840400-43851800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr15:43840800-43853200	Weak transcription	Psoas Muscle	Psoas
29	chr15:43841600-43850200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
30	chr15:43842000-43852600	Weak transcription	NHEK	skin
31	chr15:43842600-43851400	Weak transcription	Colon Smooth Muscle	Colon
32	chr15:43843200-43852600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr15:43843400-43852400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr15:43843400-43852600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr15:43845000-43850400	Weak transcription	Gastric	stomach
36	chr15:43845000-43852400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr15:43845200-43851200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr15:43845200-43851800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr15:43845400-43851400	Strong transcription	Brain Anterior Caudate	brain
40	chr15:43846600-43850800	Weak transcription	Primary T helper cells PMA-I stimulated	--
41	chr15:43846800-43851400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr15:43847200-43853000	Weak transcription	Fetal Muscle Leg	muscle
43	chr15:43847400-43851400	Weak transcription	Small Intestine	intestine
44	chr15:43848000-43850400	Weak transcription	Right Atrium	heart
45	chr15:43848000-43851000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr15:43848200-43851400	Strong transcription	Fetal Stomach	stomach
47	chr15:43848400-43850000	Strong transcription	Brain Angular Gyrus	brain
48	chr15:43848400-43851400	Weak transcription	Fetal Muscle Trunk	muscle
49	chr15:43848400-43851800	Strong transcription	Brain Inferior Temporal Lobe	brain
50	chr15:43848600-43851600	Strong transcription	Sigmoid Colon	Sigmoid Colon

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