Variant report

Variant	rs57241635
Chromosome Location	chr9:103192552-103192553
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:103187873..103189614-chr9:103191281..103192946,2	K562	blood:
2	chr9:103105076..103107773-chr9:103190189..103193187,3	MCF-7	breast:
3	chr9:101982434..101984283-chr9:103190237..103193103,2	MCF-7	breast:
4	chr9:103112020..103116853-chr9:103187928..103193300,12	MCF-7	breast:

Variant related genes	Relation type
ENSG00000066697	Chromatin interaction
ENSG00000136891	Chromatin interaction
ENSG00000119523	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs1016176	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1016177	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10989090	0.82[EUR][1000 genomes]
rs10989092	0.82[EUR][1000 genomes]
rs12237166	0.81[EUR][1000 genomes]
rs17740576	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17813447	0.88[EUR][1000 genomes]
rs17813663	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17813801	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17813854	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2026998	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2151107	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35438121	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs41274963	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4395949	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs56179916	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56313595	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56720423	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs58030694	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58698990	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs59668196	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61306839	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61386923	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7046659	0.81[EUR][1000 genomes]
rs72733393	0.87[EUR][1000 genomes]
rs72733395	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72733397	0.86[EUR][1000 genomes]
rs72735110	0.81[EUR][1000 genomes]
rs73655529	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73655530	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73655531	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73655532	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73655533	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73655534	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73655535	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73655536	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73655537	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73655539	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73655540	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73655541	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73655542	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73655543	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73655544	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73655545	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73655546	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73655547	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73655549	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73655550	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73655551	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73655553	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73655554	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73655579	0.80[AFR][1000 genomes]
rs7866623	0.89[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893623	chr9:102648036-103405197	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv825012	chr9:103152205-103256281	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv614955	chr9:103181596-103261227	ZNF genes & repeats Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs57241635	C9orf30	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:103188800-103192800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr9:103190400-103192600	Weak transcription	Pancreas	Pancrea
3	chr9:103190400-103193000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr9:103190400-103206000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr9:103190400-103214200	Weak transcription	Thymus	Thymus
6	chr9:103190600-103197400	Weak transcription	Fetal Intestine Small	intestine
7	chr9:103190600-103214400	Weak transcription	Primary B cells from cord blood	blood
8	chr9:103190600-103224600	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr9:103190800-103192600	Enhancers	Fetal Brain Male	brain
10	chr9:103190800-103192800	Enhancers	HepG2	liver
11	chr9:103190800-103200400	Weak transcription	Liver	Liver
12	chr9:103190800-103204000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr9:103190800-103204400	Weak transcription	Primary B cells from peripheral blood	blood
14	chr9:103190800-103206000	Weak transcription	Primary T cells from cord blood	blood
15	chr9:103190800-103206800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr9:103190800-103207200	Weak transcription	Fetal Lung	lung
17	chr9:103190800-103213200	Weak transcription	Primary hematopoietic stem cells	blood
18	chr9:103190800-103217600	Weak transcription	Fetal Intestine Large	intestine
19	chr9:103191000-103203400	Weak transcription	Fetal Muscle Trunk	muscle
20	chr9:103191000-103206600	Weak transcription	Colonic Mucosa	Colon
21	chr9:103191200-103204200	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr9:103191200-103214200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr9:103191400-103192600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr9:103191400-103196000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr9:103191600-103192600	Enhancers	Brain Hippocampus Middle	brain
26	chr9:103191600-103192600	Enhancers	NHLF	lung
27	chr9:103191600-103192800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr9:103191600-103192800	Enhancers	HSMM	muscle
29	chr9:103191600-103193200	Enhancers	HSMMtube	muscle
30	chr9:103191600-103194400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr9:103191600-103194800	Enhancers	Breast Myoepithelial Primary Cells	Breast
32	chr9:103191600-103195200	Weak transcription	Psoas Muscle	Psoas
33	chr9:103191600-103199400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr9:103191600-103201200	Weak transcription	Fetal Muscle Leg	muscle
35	chr9:103191600-103202000	Weak transcription	Placenta	Placenta
36	chr9:103191600-103202400	Weak transcription	Small Intestine	intestine
37	chr9:103191600-103204200	Weak transcription	Ovary	ovary
38	chr9:103191600-103204400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr9:103191600-103204400	Weak transcription	Primary T helper cells fromperipheralblood	blood
40	chr9:103191600-103204400	Weak transcription	Gastric	stomach
41	chr9:103191600-103206600	Weak transcription	Aorta	Aorta
42	chr9:103191600-103209200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr9:103191600-103209200	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr9:103191600-103212800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr9:103191600-103213000	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr9:103191600-103214400	Weak transcription	Esophagus	oesophagus
47	chr9:103191800-103192600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr9:103191800-103193000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr9:103191800-103196000	Weak transcription	Right Atrium	heart
50	chr9:103191800-103197000	Weak transcription	Fetal Heart	heart

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