Variant report

Variant	rs12913130
Chromosome Location	chr15:83690437-83690438
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:83688240..83691161-chr15:83697132..83700281,3	K562	blood:
2	chr15:83683950..83686257-chr15:83688068..83690972,3	MCF-7	breast:
3	chr15:83679667..83682766-chr15:83686991..83690446,4	MCF-7	breast:
4	chr15:83680931..83684060-chr15:83687587..83694949,8	K562	blood:
5	chr15:83679499..83683217-chr15:83687466..83692124,6	K562	blood:
6	chr15:83687509..83691091-chr15:83696720..83699538,3	K562	blood:

Variant related genes	Relation type
ENSG00000064726	Chromatin interaction
ENSG00000169609	Chromatin interaction
ENSG00000249214	Chromatin interaction
ENSG00000260608	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs10400812	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10520576	1.00[JPT][hapmap]
rs1112404	1.00[JPT][hapmap]
rs11259965	1.00[JPT][hapmap]
rs11259969	1.00[JPT][hapmap]
rs11852408	1.00[JPT][hapmap]
rs11852496	1.00[JPT][hapmap]
rs11853742	0.92[JPT][hapmap]
rs11856171	1.00[JPT][hapmap]
rs11857641	1.00[JPT][hapmap]
rs11858074	0.95[ASN][1000 genomes]
rs11858377	1.00[JPT][hapmap]
rs12439782	0.87[EUR][1000 genomes]
rs12440386	1.00[JPT][hapmap]
rs12441585	1.00[JPT][hapmap]
rs12443109	1.00[JPT][hapmap]
rs12591855	1.00[JPT][hapmap]
rs12592391	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12593316	0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs12593638	0.91[JPT][hapmap]
rs12594496	1.00[JPT][hapmap]
rs12595330	1.00[JPT][hapmap]
rs12899522	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12900411	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12901811	0.95[ASN][1000 genomes]
rs12902721	0.82[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs12903066	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12904695	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12906027	0.95[ASN][1000 genomes]
rs12906626	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12907032	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12911706	0.95[ASN][1000 genomes]
rs12911891	0.95[ASN][1000 genomes]
rs12917594	0.94[ASN][1000 genomes]
rs13329195	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13329269	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17158080	1.00[JPT][hapmap]
rs17158127	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs17294476	0.90[JPT][hapmap]
rs17507300	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs17567151	1.00[JPT][hapmap]
rs17567869	1.00[JPT][hapmap]
rs17568459	1.00[JPT][hapmap]
rs2034617	0.91[JPT][hapmap]
rs2034618	1.00[JPT][hapmap]
rs2084839	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2381030	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28436027	0.91[JPT][hapmap]
rs28485801	0.97[ASN][1000 genomes]
rs28580677	0.97[ASN][1000 genomes]
rs3087804	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34869943	0.92[ASN][1000 genomes]
rs35207081	0.95[ASN][1000 genomes]
rs35627116	0.94[ASN][1000 genomes]
rs36038412	0.95[ASN][1000 genomes]
rs4079029	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4563011	1.00[JPT][hapmap]
rs61375537	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6603044	0.96[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6603046	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6603047	0.91[JPT][hapmap]
rs66606849	0.95[ASN][1000 genomes]
rs67482297	0.95[ASN][1000 genomes]
rs67822554	0.95[ASN][1000 genomes]
rs7163516	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7164083	0.83[JPT][hapmap]
rs7165114	1.00[JPT][hapmap]
rs7165978	1.00[JPT][hapmap]
rs7166645	0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7170547	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7172665	0.96[CEU][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7177599	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7181169	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7495911	1.00[JPT][hapmap]
rs750214	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7757	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs8023669	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap]
rs8027193	1.00[JPT][hapmap]
rs8027577	1.00[JPT][hapmap]
rs8031896	0.98[ASN][1000 genomes]
rs8035810	1.00[JPT][hapmap]
rs8037783	1.00[JPT][hapmap]
rs8038486	1.00[JPT][hapmap]
rs8040457	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8040998	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8043224	1.00[JPT][hapmap]
rs9646239	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs965264	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1040336	chr15:83578947-83768335	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv482308	chr15:83584918-83747362	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers 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	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12913130	BTBD1	cis	Nerve Tibial	GTEx
rs12913130	HDGFRP3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:83681000-83700200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr15:83681000-83705000	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr15:83681200-83693400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr15:83681200-83698200	Weak transcription	NHLF	lung
5	chr15:83681200-83710200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr15:83681400-83698000	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr15:83681400-83698400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr15:83681600-83698200	Weak transcription	Brain Cingulate Gyrus	brain
9	chr15:83681600-83698200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr15:83681600-83732000	Weak transcription	Stomach Mucosa	stomach
11	chr15:83682000-83708400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr15:83682200-83708600	Weak transcription	Fetal Heart	heart
13	chr15:83683000-83691000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr15:83683000-83723000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr15:83683400-83726600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr15:83684000-83691000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr15:83684200-83690800	Strong transcription	GM12878-XiMat	blood
18	chr15:83684200-83691200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr15:83684200-83691200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr15:83684200-83691400	Strong transcription	Fetal Muscle Trunk	muscle
21	chr15:83684400-83690800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr15:83684400-83691000	Strong transcription	Primary B cells from peripheral blood	blood
23	chr15:83684400-83691000	Strong transcription	Hela-S3	cervix
24	chr15:83684600-83691000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr15:83684600-83691000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr15:83684600-83691200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr15:83684600-83691200	Strong transcription	Fetal Thymus	thymus
28	chr15:83684600-83693000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
29	chr15:83684600-83695200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr15:83685200-83691000	Strong transcription	HUES64 Cell Line	embryonic stem cell
31	chr15:83685400-83690800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr15:83685400-83690800	Strong transcription	HUES48 Cell Line	embryonic stem cell
33	chr15:83685600-83691000	Strong transcription	HUES6 Cell Line	embryonic stem cell
34	chr15:83685600-83693800	Strong transcription	Fetal Muscle Leg	muscle
35	chr15:83685800-83690600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr15:83685800-83690800	Strong transcription	Colon Smooth Muscle	Colon
37	chr15:83685800-83691000	Strong transcription	Primary T helper cells PMA-I stimulated	--
38	chr15:83685800-83691000	Strong transcription	Liver	Liver
39	chr15:83685800-83691000	Strong transcription	Placenta	Placenta
40	chr15:83685800-83691000	Strong transcription	Dnd41	blood
41	chr15:83686600-83690800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr15:83686600-83695800	Weak transcription	Brain Hippocampus Middle	brain
43	chr15:83686800-83690800	Strong transcription	Primary T cells from cord blood	blood
44	chr15:83687000-83708200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr15:83687200-83690800	Strong transcription	HepG2	liver
46	chr15:83687200-83697000	Strong transcription	Fetal Intestine Large	intestine
47	chr15:83687600-83691000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr15:83687600-83698400	Weak transcription	Brain Substantia Nigra	brain
49	chr15:83687600-83701200	Weak transcription	Fetal Brain Female	brain
50	chr15:83687600-83709600	Weak transcription	Brain Angular Gyrus	brain

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