Variant report

Variant	rs4744380
Chromosome Location	chr9:97597317-97597318
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:97594651..97597412-chr9:97683309..97685774,2	MCF-7	breast:
2	chr9:97591789..97593682-chr9:97596295..97598175,2	K562	blood:
3	chr9:97584341..97586520-chr9:97595155..97598117,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000148120	Chromatin interaction

Extended variants
information (count: 123 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:122)

rs_ID	r²[population]
rs10121865	0.80[CEU][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10122127	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10217427	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10512234	1.00[JPT][hapmap]
rs10512236	1.00[JPT][hapmap]
rs10732405	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];0.94[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10732406	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10733755	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10739986	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10761355	0.80[CEU][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10761359	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10821405	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10993329	1.00[JPT][hapmap]
rs10993340	0.90[JPT][hapmap]
rs10993348	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10993351	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap]
rs1228614	0.80[CEU][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12336437	0.86[JPT][hapmap]
rs12337706	1.00[JPT][hapmap]
rs12337992	1.00[JPT][hapmap]
rs12339275	0.80[CEU][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12340251	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12341764	1.00[JPT][hapmap]
rs12341814	1.00[JPT][hapmap]
rs12343530	1.00[JPT][hapmap]
rs12344157	1.00[JPT][hapmap];0.83[MKK][hapmap]
rs12344537	0.80[CEU][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12347744	1.00[JPT][hapmap]
rs12348060	1.00[JPT][hapmap]
rs12352276	0.80[CEU][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12352600	1.00[JPT][hapmap]
rs12553690	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12684703	0.80[CEU][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13285343	0.80[CEU][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs16911661	0.80[CEU][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs16911670	1.00[JPT][hapmap]
rs16911713	1.00[JPT][hapmap];0.83[MKK][hapmap]
rs1810772	0.86[EUR][1000 genomes]
rs181488	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs187163	0.80[CEU][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs193292	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2119954	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2165715	1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes]
rs2165716	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2304884	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2406899	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs242259	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2584803	0.80[CEU][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2584804	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2767403	0.80[CEU][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2767404	0.80[CEU][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28647286	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34940574	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs356122	0.80[CEU][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs356123	0.80[CEU][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs356124	0.80[CEU][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs356126	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs356127	0.80[CEU][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs356129	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs356130	0.80[CEU][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs356134	0.80[CEU][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs356135	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];0.86[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs356137	0.80[CEU][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs356138	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs356140	0.80[CEU][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs356142	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs356143	0.80[CEU][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs356146	0.80[CEU][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs374708	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs376902	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];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs380205	0.80[CEU][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3808890	1.00[JPT][hapmap]
rs384039	1.00[CEU][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3858087	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3858088	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs389365	0.80[CEU][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs396538	0.80[CEU][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs397617	0.80[CEU][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs400231	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs405110	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs415016	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs418764	0.80[CEU][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs439052	0.80[CEU][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4437717	0.80[CEU][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4537361	0.80[CEU][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs471161	0.80[CEU][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4744377	0.80[CEU][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4744379	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4744383	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4744388	0.96[AFR][1000 genomes]
rs55795862	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs55914113	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs55926255	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs57504746	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs58042095	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6479565	0.87[EUR][1000 genomes]
rs6479570	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6479571	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6479572	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6479574	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6479577	0.94[AFR][1000 genomes]
rs672012	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs67625382	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7025100	0.90[YRI][hapmap]
rs7025234	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7028317	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7030617	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7031172	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.81[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7031518	0.83[AMR][1000 genomes]
rs7041982	0.85[EUR][1000 genomes]
rs7045387	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7047864	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs732141	0.80[CEU][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7853126	0.80[CEU][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7861358	0.80[CEU][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7862700	0.80[CEU][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7866487	1.00[JPT][hapmap]
rs7869666	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs913182	0.87[EUR][1000 genomes]
rs925813	1.00[JPT][hapmap]
rs9409806	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9987803	1.00[JPT][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893596	chr9:97321172-97598966	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4744380	C9orf3	cis	lymphoblastoid	seeQTL
rs4744380	ASPN	cis	parietal	SCAN
rs4744380	FAM120A	cis	parietal	SCAN
rs4744380	hCG_2003663	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97570000-97601400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr9:97571800-97622600	Weak transcription	Primary B cells from cord blood	blood
3	chr9:97572000-97601600	Weak transcription	Primary T cells fromperipheralblood	blood
4	chr9:97580600-97600200	Weak transcription	Primary hematopoietic stem cells	blood
5	chr9:97581800-97609600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr9:97582000-97599400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr9:97585000-97609600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr9:97589200-97598800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr9:97589200-97600400	Weak transcription	Primary T cells from cord blood	blood
10	chr9:97589200-97602000	Weak transcription	Lung	lung
11	chr9:97589200-97605400	Weak transcription	Spleen	Spleen
12	chr9:97589200-97609400	Weak transcription	Pancreas	Pancrea
13	chr9:97589200-97622400	Weak transcription	Aorta	Aorta
14	chr9:97589400-97598600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr9:97590400-97598600	Weak transcription	Fetal Intestine Large	intestine
16	chr9:97590400-97602000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr9:97590600-97609600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr9:97590600-97616000	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr9:97591000-97609200	Weak transcription	Osteobl	bone
20	chr9:97592200-97599800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr9:97592200-97608400	Weak transcription	HSMMtube	muscle
22	chr9:97592200-97609400	Weak transcription	NHDF-Ad	bronchial
23	chr9:97592600-97599200	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr9:97594800-97597600	Weak transcription	A549	lung
25	chr9:97595000-97599600	Weak transcription	HSMM	muscle
26	chr9:97597000-97598400	Enhancers	HepG2	liver
27	chr9:97597200-97603000	Weak transcription	Liver	Liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links