Variant report

Variant	rs13329195
Chromosome Location	chr15:83708085-83708086
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:83668024..83670019-chr15:83707664..83709687,2	K562	blood:
2	chr15:83679479..83681361-chr15:83707493..83709575,2	MCF-7	breast:
3	chr15:83706535..83711494-chr15:83875161..83878411,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000169609	Chromatin interaction
ENSG00000166503	Chromatin interaction

Extended variants
information (count: 92 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs10400812	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[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	0.91[JPT][hapmap]
rs11856171	1.00[JPT][hapmap]
rs11857428	1.00[JPT][hapmap]
rs11857641	1.00[JPT][hapmap]
rs11858074	0.95[ASN][1000 genomes]
rs11858377	1.00[JPT][hapmap]
rs12439782	0.89[EUR][1000 genomes]
rs12440386	1.00[JPT][hapmap]
rs12441585	0.82[CHD][hapmap];1.00[JPT][hapmap]
rs12443109	1.00[JPT][hapmap]
rs12591855	1.00[JPT][hapmap]
rs12592391	1.00[CHB][hapmap];0.84[CHD][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[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12900411	1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12901811	0.95[ASN][1000 genomes]
rs12902721	0.82[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs12903066	1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12904695	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12906027	0.95[ASN][1000 genomes]
rs12906626	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12907032	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12911706	0.95[ASN][1000 genomes]
rs12911891	0.95[ASN][1000 genomes]
rs12913130	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]
rs12917594	0.94[ASN][1000 genomes]
rs13329269	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17158080	0.82[CHD][hapmap];1.00[JPT][hapmap]
rs17158127	1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs17294476	0.90[JPT][hapmap]
rs17507300	1.00[CHB][hapmap];1.00[CHD][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	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2381030	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28436027	0.91[JPT][hapmap]
rs28485801	0.97[ASN][1000 genomes]
rs28580677	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3087804	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.96[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[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[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4563011	1.00[JPT][hapmap]
rs61375537	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6603044	0.94[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.83[LWK][hapmap];0.96[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6603046	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.95[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	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7164083	0.82[JPT][hapmap]
rs7165114	1.00[JPT][hapmap]
rs7165978	1.00[JPT][hapmap]
rs7166645	0.90[AFR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7170547	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7172665	1.00[CEU][hapmap];0.97[GIH][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7177599	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7180407	1.00[JPT][hapmap]
rs7181169	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7495911	1.00[JPT][hapmap]
rs750214	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7757	1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs8023669	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];1.00[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	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8040998	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.82[LWK][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs13329195	BTBD1	cis	parietal	SCAN
rs13329195	WHAMM	cis	cerebellum	SCAN
rs13329195	ARNT2	cis	cerebellum	SCAN
rs13329195	BTBD1	cis	Nerve Tibial	GTEx
rs13329195	HDGFRP3	Cis_1M	lymphoblastoid	RTeQTL
rs13329195	TM6SF1	cis	cerebellum	SCAN
rs13329195	BTBD1	cis	lymphoblastoid	seeQTL
rs13329195	WHAMM	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:83681200-83710200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr15:83681600-83732000	Weak transcription	Stomach Mucosa	stomach
3	chr15:83682000-83708400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr15:83682200-83708600	Weak transcription	Fetal Heart	heart
5	chr15:83683000-83723000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr15:83683400-83726600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr15:83687000-83708200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr15:83687600-83709600	Weak transcription	Brain Angular Gyrus	brain
9	chr15:83688800-83708800	Weak transcription	Fetal Brain Male	brain
10	chr15:83689400-83708600	Weak transcription	NHEK	skin
11	chr15:83690000-83708200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr15:83690000-83708800	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr15:83695400-83714600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr15:83695800-83715400	Weak transcription	HSMMtube	muscle
15	chr15:83696400-83708200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr15:83697800-83721000	Strong transcription	Fetal Intestine Large	intestine
17	chr15:83698400-83708600	Weak transcription	Brain Anterior Caudate	brain
18	chr15:83698600-83708200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr15:83698600-83709600	Weak transcription	Colon Smooth Muscle	Colon
20	chr15:83698800-83708200	Weak transcription	HUVEC	blood vessel
21	chr15:83698800-83708600	Weak transcription	HMEC	breast
22	chr15:83698800-83712000	Weak transcription	Colonic Mucosa	Colon
23	chr15:83699000-83708200	Weak transcription	Left Ventricle	heart
24	chr15:83699000-83708200	Weak transcription	Ovary	ovary
25	chr15:83699000-83708200	Weak transcription	Right Ventricle	heart
26	chr15:83699000-83708200	Weak transcription	Spleen	Spleen
27	chr15:83699000-83708200	Weak transcription	NHLF	lung
28	chr15:83699000-83708400	Weak transcription	Pancreas	Pancrea
29	chr15:83699000-83708600	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr15:83699000-83708600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr15:83699000-83708600	Weak transcription	Placenta	Placenta
32	chr15:83699000-83708800	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr15:83699000-83709000	Weak transcription	Small Intestine	intestine
34	chr15:83699000-83710000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr15:83699000-83712000	Weak transcription	Gastric	stomach
36	chr15:83699000-83715800	Weak transcription	Brain Substantia Nigra	brain
37	chr15:83699000-83716800	Weak transcription	Aorta	Aorta
38	chr15:83699000-83725800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr15:83699200-83708600	Weak transcription	Osteobl	bone
40	chr15:83699200-83708800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
41	chr15:83699400-83708200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr15:83699400-83708800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr15:83699400-83708800	Weak transcription	NH-A	brain
44	chr15:83699600-83708600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr15:83699800-83709000	Weak transcription	Hela-S3	cervix
46	chr15:83700400-83708600	Weak transcription	Esophagus	oesophagus
47	chr15:83700400-83734400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr15:83701400-83708200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr15:83701600-83708200	Weak transcription	Thymus	Thymus
50	chr15:83701600-83732800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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