Variant report

Variant	rs8023669
Chromosome Location	chr15:83720657-83720658
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:83718422..83721272-chr15:83727802..83729791,2	MCF-7	breast:
2	chr15:83683189..83685982-chr15:83719476..83721962,2	MCF-7	breast:
3	chr15:83719346..83723182-chr15:83733167..83737107,5	MCF-7	breast:
4	chr15:83715424..83718064-chr15:83719632..83721624,3	K562	blood:
5	chr15:83715424..83717754-chr15:83719632..83721290,2	K562	blood:
6	chr15:83680450..83681968-chr15:83719414..83722223,2	K562	blood:

Variant related genes	Relation type
ENSG00000260608	Chromatin interaction
ENSG00000249214	Chromatin interaction
ENSG00000064726	Chromatin interaction
ENSG00000263643	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10400812	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap]
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]
rs11858377	1.00[JPT][hapmap]
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]
rs12593316	0.91[JPT][hapmap]
rs12593638	0.91[JPT][hapmap]
rs12594496	1.00[JPT][hapmap]
rs12595330	1.00[JPT][hapmap]
rs12900411	1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap]
rs12902721	0.82[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap]
rs12903066	1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap]
rs12907032	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];1.00[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap]
rs12913130	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap]
rs13329195	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]
rs17158080	0.82[CHD][hapmap];1.00[JPT][hapmap]
rs17158127	1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap]
rs17294476	0.90[JPT][hapmap]
rs17507300	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
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]
rs2381030	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.96[MEX][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap]
rs28436027	0.91[JPT][hapmap]
rs3087804	0.94[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.91[MEX][hapmap];0.95[MKK][hapmap];0.98[TSI][hapmap];0.89[YRI][hapmap]
rs4079029	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap]
rs4563011	1.00[JPT][hapmap]
rs6603044	0.94[ASW][hapmap];0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.83[LWK][hapmap];0.91[MEX][hapmap];0.95[MKK][hapmap];0.98[TSI][hapmap];0.89[YRI][hapmap]
rs6603046	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap]
rs6603047	0.91[JPT][hapmap]
rs7164083	0.82[JPT][hapmap]
rs7165114	1.00[JPT][hapmap]
rs7165978	1.00[JPT][hapmap]
rs7172665	0.96[CEU][hapmap];0.97[GIH][hapmap];0.87[MEX][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap]
rs7177599	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs7180407	1.00[JPT][hapmap]
rs7495911	1.00[JPT][hapmap]
rs750214	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap]
rs7757	1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap]
rs8027193	1.00[JPT][hapmap]
rs8027577	1.00[JPT][hapmap]
rs8035810	1.00[JPT][hapmap]
rs8037783	1.00[JPT][hapmap]
rs8038486	1.00[JPT][hapmap]
rs8040998	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.81[LWK][hapmap];0.91[MEX][hapmap];0.91[MKK][hapmap];0.98[TSI][hapmap];0.93[YRI][hapmap]
rs8043224	1.00[JPT][hapmap]
rs9646239	1.00[CHB][hapmap];1.00[JPT][hapmap]
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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs8023669	ARNT2	cis	cerebellum	SCAN
rs8023669	TM6SF1	cis	cerebellum	SCAN
rs8023669	BTBD1	cis	Skin Sun Exposed Lower leg	GTEx
rs8023669	WHAMM	cis	cerebellum	SCAN
rs8023669	BTBD1	cis	lymphoblastoid	seeQTL
rs8023669	BTBD1	cis	parietal	SCAN
rs8023669	HDGFRP3	Cis_1M	lymphoblastoid	RTeQTL
rs8023669	WHAMM	cis	parietal	SCAN
rs8023669	BTBD1	cis	Nerve Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:83681600-83732000	Weak transcription	Stomach Mucosa	stomach
2	chr15:83683000-83723000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr15:83683400-83726600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr15:83697800-83721000	Strong transcription	Fetal Intestine Large	intestine
5	chr15:83699000-83725800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr15:83700400-83734400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr15:83701600-83732800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr15:83705000-83720800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr15:83705000-83725800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr15:83705000-83731000	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr15:83705600-83721400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr15:83706000-83725400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr15:83706800-83726600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr15:83707000-83725400	Strong transcription	HUES64 Cell Line	embryonic stem cell
15	chr15:83707400-83725400	Strong transcription	HUES6 Cell Line	embryonic stem cell
16	chr15:83708000-83722000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
17	chr15:83708000-83725400	Strong transcription	HUES48 Cell Line	embryonic stem cell
18	chr15:83708600-83726000	Strong transcription	Primary monocytes fromperipheralblood	blood
19	chr15:83708800-83726400	Strong transcription	Primary T cells fromperipheralblood	blood
20	chr15:83708800-83726600	Weak transcription	Pancreas	Pancrea
21	chr15:83709000-83726600	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr15:83709000-83726600	Weak transcription	Fetal Brain Male	brain
23	chr15:83709200-83724400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr15:83709200-83727000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr15:83709600-83730800	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr15:83710400-83722800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr15:83710600-83722000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr15:83710600-83723800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr15:83710600-83723800	Weak transcription	Brain Angular Gyrus	brain
30	chr15:83710600-83730200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr15:83710600-83730200	Weak transcription	Esophagus	oesophagus
32	chr15:83710800-83725800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr15:83711400-83720800	Strong transcription	K562	blood
34	chr15:83711800-83724800	Strong transcription	Hela-S3	cervix
35	chr15:83711800-83725000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
36	chr15:83712200-83725800	Weak transcription	Right Ventricle	heart
37	chr15:83712400-83722600	Weak transcription	Brain Germinal Matrix	brain
38	chr15:83712600-83722800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr15:83713400-83725600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr15:83713600-83726600	Weak transcription	Gastric	stomach
41	chr15:83714200-83730200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr15:83714400-83720800	Weak transcription	Fetal Intestine Small	intestine
43	chr15:83714400-83726600	Strong transcription	Primary T helper cells fromperipheralblood	blood
44	chr15:83714800-83725800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
45	chr15:83715200-83725400	Strong transcription	Liver	Liver
46	chr15:83715600-83725000	Strong transcription	Duodenum Mucosa	Duodenum
47	chr15:83716200-83725400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr15:83716400-83721200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr15:83716600-83721200	Strong transcription	Skeletal Muscle Female	skeletal muscle
50	chr15:83717000-83725600	Weak transcription	Fetal Heart	heart

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