Variant report

Variant	rs17507300
Chromosome Location	chr15:83722059-83722060
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:83714522..83717399-chr15:83720662..83723251,3	MCF-7	breast:
2	chr15:83719346..83723182-chr15:83733167..83737107,5	MCF-7	breast:
3	chr15:83714861..83717346-chr15:83721715..83724046,2	K562	blood:
4	chr15:83251945..83254167-chr15:83721168..83723752,2	K562	blood:
5	chr15:83680450..83681968-chr15:83719414..83722223,2	K562	blood:

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

Extended variants
information (count: 89 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10400812	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[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	0.97[ASN][1000 genomes]
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];0.82[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12593316	0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs12593638	0.91[JPT][hapmap]
rs12594496	1.00[JPT][hapmap]
rs12595330	1.00[JPT][hapmap]
rs12899522	0.91[ASN][1000 genomes]
rs12900411	1.00[CHB][hapmap];0.82[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12901811	0.97[ASN][1000 genomes]
rs12902721	0.82[CHB][hapmap];0.84[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12903066	1.00[CHB][hapmap];0.84[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12904695	0.98[ASN][1000 genomes]
rs12906027	0.97[ASN][1000 genomes]
rs12906626	0.98[ASN][1000 genomes]
rs12907032	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs12911706	0.97[ASN][1000 genomes]
rs12911891	0.97[ASN][1000 genomes]
rs12913130	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs12917594	0.95[ASN][1000 genomes]
rs13329195	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs13329269	0.91[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];0.97[ASN][1000 genomes]
rs17294476	0.90[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]
rs2084839	0.86[ASN][1000 genomes]
rs2381030	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs28436027	0.91[JPT][hapmap]
rs28485801	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28580677	0.98[ASN][1000 genomes]
rs3087804	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs34869943	0.94[ASN][1000 genomes]
rs35207081	0.97[ASN][1000 genomes]
rs35627116	0.95[ASN][1000 genomes]
rs36038412	0.97[ASN][1000 genomes]
rs4079029	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4563011	1.00[JPT][hapmap]
rs6603044	0.82[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];0.98[ASN][1000 genomes]
rs6603046	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6603047	0.91[JPT][hapmap]
rs66606849	0.97[ASN][1000 genomes]
rs67482297	0.97[ASN][1000 genomes]
rs67822554	0.97[ASN][1000 genomes]
rs7163516	0.92[ASN][1000 genomes]
rs7164083	0.82[JPT][hapmap]
rs7165114	1.00[JPT][hapmap]
rs7165978	1.00[JPT][hapmap]
rs7166645	0.97[ASN][1000 genomes]
rs7170547	0.97[ASN][1000 genomes]
rs7177599	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7180407	1.00[JPT][hapmap]
rs7181169	0.98[ASN][1000 genomes]
rs7495911	1.00[JPT][hapmap]
rs750214	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7757	1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs8023669	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs8027193	1.00[JPT][hapmap]
rs8027577	1.00[JPT][hapmap]
rs8031896	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs8035810	1.00[JPT][hapmap]
rs8037783	1.00[JPT][hapmap]
rs8038486	1.00[JPT][hapmap]
rs8040457	0.97[ASN][1000 genomes]
rs8040998	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.98[ASN][1000 genomes]
rs8043224	1.00[JPT][hapmap]
rs9646239	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs17507300	CIB2	cis	cerebellum	SCAN
rs17507300	BTBD1	cis	lymphoblastoid	seeQTL
rs17507300	WHAMM	cis	parietal	SCAN
rs17507300	CHRNA3	cis	cerebellum	SCAN
rs17507300	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	chr15:83681600-83732000	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	chr15:83699000-83725800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr15:83700400-83734400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr15:83701600-83732800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr15:83705000-83725800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr15:83705000-83731000	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr15:83706000-83725400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr15:83706800-83726600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr15:83707000-83725400	Strong transcription	HUES64 Cell Line	embryonic stem cell
12	chr15:83707400-83725400	Strong transcription	HUES6 Cell Line	embryonic stem cell
13	chr15:83708000-83725400	Strong transcription	HUES48 Cell Line	embryonic stem cell
14	chr15:83708600-83726000	Strong transcription	Primary monocytes fromperipheralblood	blood
15	chr15:83708800-83726400	Strong transcription	Primary T cells fromperipheralblood	blood
16	chr15:83708800-83726600	Weak transcription	Pancreas	Pancrea
17	chr15:83709000-83726600	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr15:83709000-83726600	Weak transcription	Fetal Brain Male	brain
19	chr15:83709200-83724400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr15:83709200-83727000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr15:83709600-83730800	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr15:83710400-83722800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr15:83710600-83723800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr15:83710600-83723800	Weak transcription	Brain Angular Gyrus	brain
25	chr15:83710600-83730200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr15:83710600-83730200	Weak transcription	Esophagus	oesophagus
27	chr15:83710800-83725800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr15:83711800-83724800	Strong transcription	Hela-S3	cervix
29	chr15:83711800-83725000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
30	chr15:83712200-83725800	Weak transcription	Right Ventricle	heart
31	chr15:83712400-83722600	Weak transcription	Brain Germinal Matrix	brain
32	chr15:83712600-83722800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr15:83713400-83725600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr15:83713600-83726600	Weak transcription	Gastric	stomach
35	chr15:83714200-83730200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr15:83714400-83726600	Strong transcription	Primary T helper cells fromperipheralblood	blood
37	chr15:83714800-83725800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
38	chr15:83715200-83725400	Strong transcription	Liver	Liver
39	chr15:83715600-83725000	Strong transcription	Duodenum Mucosa	Duodenum
40	chr15:83716200-83725400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr15:83717000-83725600	Weak transcription	Fetal Heart	heart
42	chr15:83717000-83726400	Weak transcription	Small Intestine	intestine
43	chr15:83717000-83726800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr15:83717200-83724400	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr15:83717200-83724600	Weak transcription	Colon Smooth Muscle	Colon
46	chr15:83717200-83725600	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr15:83717400-83722200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr15:83717400-83722800	Weak transcription	Psoas Muscle	Psoas
49	chr15:83717400-83725600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
50	chr15:83717400-83725800	Weak transcription	Rectal Smooth Muscle	rectum

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