Variant report

Variant	rs10732405
Chromosome Location	chr9:97586542-97586543
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:97562492..97588737-chr9:97670126..97691056,102	MCF-7	breast:
2	chr9:97572097..97590438-chr9:97672990..97690806,63	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];1.00[MEX][hapmap];0.93[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];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10217427	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10512234	1.00[JPT][hapmap]
rs10512236	1.00[JPT][hapmap]
rs10732406	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10733755	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10739986	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10761355	0.80[CEU][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10761359	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10821405	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10993329	1.00[JPT][hapmap]
rs10993340	0.90[JPT][hapmap]
rs10993348	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10993351	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[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];1.00[MEX][hapmap];0.93[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];1.00[MEX][hapmap];0.93[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	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][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	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2165715	1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.92[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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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];0.84[ASN][1000 genomes]
rs2584803	0.80[CEU][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2584804	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2767403	0.80[CEU][hapmap];1.00[MEX][hapmap];0.93[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];1.00[MEX][hapmap];0.93[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];0.93[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];0.93[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs356137	0.80[CEU][hapmap];1.00[MEX][hapmap];0.93[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	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs356143	0.80[CEU][hapmap];1.00[MEX][hapmap];0.93[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];1.00[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs380205	0.80[CEU][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3808890	1.00[JPT][hapmap]
rs384039	1.00[CEU][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][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];1.00[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs397617	0.80[CEU][hapmap];1.00[MEX][hapmap];0.93[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	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[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];1.00[MEX][hapmap];0.93[TSI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs471161	0.80[CEU][hapmap];1.00[MEX][hapmap];0.93[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]
rs4744380	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]
rs4744383	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4744388	0.92[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	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6479571	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6479572	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6479574	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6479577	0.90[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];0.81[AFR][1000 genomes]
rs7025234	0.95[AMR][1000 genomes];0.93[EUR][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];0.87[MEX][hapmap];0.93[MKK][hapmap];0.93[TSI][hapmap];0.81[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[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];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[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];1.00[MEX][hapmap];0.93[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];0.86[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
rs10732405	ASPN	cis	parietal	SCAN
rs10732405	hCG_2003663	Cis_1M	lymphoblastoid	RTeQTL
rs10732405	FAM120A	cis	parietal	SCAN
rs10732405	C9orf3	cis	lymphoblastoid	seeQTL

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97563600-97594400	Weak transcription	Primary T helper cells PMA-I stimulated	--
2	chr9:97564000-97589200	Weak transcription	Primary T helper cells fromperipheralblood	blood
3	chr9:97565200-97587000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr9:97567400-97593400	Weak transcription	Thymus	Thymus
5	chr9:97568600-97589000	Weak transcription	Liver	Liver
6	chr9:97568800-97586800	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr9:97569200-97589000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr9:97569400-97587600	Weak transcription	Brain Germinal Matrix	brain
9	chr9:97569400-97589600	Weak transcription	Fetal Thymus	thymus
10	chr9:97570000-97594400	Weak transcription	Dnd41	blood
11	chr9:97570000-97601400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr9:97570400-97590400	Weak transcription	Duodenum Mucosa	Duodenum
13	chr9:97571800-97622600	Weak transcription	Primary B cells from cord blood	blood
14	chr9:97572000-97601600	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr9:97572400-97588600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr9:97572600-97593600	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr9:97574200-97590000	Weak transcription	Fetal Intestine Large	intestine
18	chr9:97574400-97588600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr9:97575200-97587600	Weak transcription	Stomach Smooth Muscle	stomach
20	chr9:97575400-97586800	Weak transcription	Colon Smooth Muscle	Colon
21	chr9:97576000-97588400	Weak transcription	Right Ventricle	heart
22	chr9:97576200-97588400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr9:97580400-97590600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr9:97580600-97587800	Weak transcription	Adipose Nuclei	Adipose
25	chr9:97580600-97588600	Weak transcription	Gastric	stomach
26	chr9:97580600-97588600	Weak transcription	Pancreas	Pancrea
27	chr9:97580600-97600200	Weak transcription	Primary hematopoietic stem cells	blood
28	chr9:97581800-97588400	Weak transcription	Spleen	Spleen
29	chr9:97581800-97588600	Weak transcription	Esophagus	oesophagus
30	chr9:97581800-97591800	Weak transcription	Small Intestine	intestine
31	chr9:97581800-97609600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr9:97582000-97587400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr9:97582000-97587400	Weak transcription	Fetal Muscle Trunk	muscle
34	chr9:97582000-97588400	Weak transcription	Left Ventricle	heart
35	chr9:97582000-97599400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr9:97582200-97587200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr9:97582200-97587200	Weak transcription	Right Atrium	heart
38	chr9:97582200-97587400	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr9:97582200-97588600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr9:97582200-97588600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr9:97582200-97594000	Weak transcription	NHEK	skin
42	chr9:97583800-97590200	Weak transcription	Primary B cells from peripheral blood	blood
43	chr9:97584000-97587400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr9:97584000-97590400	Enhancers	Brain Hippocampus Middle	brain
45	chr9:97584200-97587600	Enhancers	Skeletal Muscle Male	skeletal muscle
46	chr9:97584200-97588400	Enhancers	HSMMtube	muscle
47	chr9:97584200-97593800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr9:97584400-97588000	Enhancers	Stomach Mucosa	stomach
49	chr9:97584600-97586800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr9:97584600-97586800	Weak transcription	Fetal Muscle Leg	muscle

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