Variant report

Variant	rs9591249
Chromosome Location	chr13:49832383-49832384
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:49829443..49832408-chr13:49849139..49850660,2	MCF-7	breast:
2	chr13:49829901..49832878-chr13:49837341..49839514,2	K562	blood:
3	chr13:49824887..49828830-chr13:49829772..49832807,6	K562	blood:

Extended variants
information (count: 82 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10459375	0.89[EUR][1000 genomes]
rs10459376	0.90[EUR][1000 genomes]
rs11619804	0.82[CHB][hapmap];0.81[CHD][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs11838927	0.86[ASN][1000 genomes]
rs11843587	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12385878	0.81[EUR][1000 genomes]
rs12585196	0.96[CEU][hapmap];0.94[GIH][hapmap];0.80[MEX][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs1555672	0.92[CEU][hapmap];0.81[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs1924659	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.86[YRI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1924660	1.00[CEU][hapmap];0.83[CHB][hapmap];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1924661	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2038759	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2147398	1.00[CEU][hapmap];0.94[GIH][hapmap];0.97[TSI][hapmap];0.84[EUR][1000 genomes]
rs2181905	0.86[AFR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2274149	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2274150	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2407521	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];0.97[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2407607	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2407608	1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2407609	0.92[CEU][hapmap];0.94[GIH][hapmap];0.85[MEX][hapmap];0.83[TSI][hapmap]
rs3087770	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3751418	0.83[JPT][hapmap]
rs3764131	0.94[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];0.94[GIH][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4245351	1.00[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4941637	1.00[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4942809	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4942811	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4942812	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.86[YRI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4942815	0.96[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6561511	1.00[CEU][hapmap];0.85[CHB][hapmap];0.92[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs719614	1.00[CEU][hapmap];0.83[CHB][hapmap];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7320595	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7320745	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7326181	0.87[EUR][1000 genomes]
rs7326191	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7328063	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs7330892	0.96[CEU][hapmap];0.81[CHB][hapmap];0.89[JPT][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7334929	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7984689	1.00[CEU][hapmap];0.83[CHB][hapmap];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7988621	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7997545	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.90[EUR][1000 genomes]
rs7999710	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9316434	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9316437	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9316439	0.91[CEU][hapmap]
rs9526532	0.82[CHB][hapmap];0.83[CHD][hapmap]
rs9526533	1.00[CEU][hapmap];0.83[CHB][hapmap];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9526534	1.00[CEU][hapmap];0.83[CHB][hapmap];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9526537	0.84[EUR][1000 genomes]
rs9526538	0.85[EUR][1000 genomes]
rs9526539	0.88[EUR][1000 genomes]
rs9535173	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9535174	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9535177	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9535180	0.80[CHB][hapmap];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9535181	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9535182	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9535184	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9535185	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9535190	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9535192	0.83[EUR][1000 genomes]
rs9535193	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];0.97[GIH][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.99[MKK][hapmap];0.97[TSI][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9535194	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9535197	1.00[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9535198	0.96[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9535199	0.96[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9535200	0.86[ASN][1000 genomes]
rs9562873	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9568174	0.85[EUR][1000 genomes]
rs9568176	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9568177	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9568179	0.88[EUR][1000 genomes]
rs9568181	0.88[EUR][1000 genomes]
rs9568182	0.86[EUR][1000 genomes]
rs9596077	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9596078	0.89[EUR][1000 genomes]
rs9596079	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9596080	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs9596082	0.83[ASN][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	nsv1049117	chr13:49089476-49928945	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv832607	chr13:49756458-49920894	Flanking Bivalent TSS/Enh Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv900069	chr13:49815405-49976393	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9591249	LCP1	cis	parietal	SCAN
rs9591249	CAB39L	cis	cerebellum	SCAN
rs9591249	RCBTB1	cis	parietal	SCAN

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:49823000-49833600	Weak transcription	Esophagus	oesophagus
2	chr13:49823000-49833600	Weak transcription	Lung	lung
3	chr13:49823000-49833600	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr13:49823000-49833800	Weak transcription	Brain Cingulate Gyrus	brain
5	chr13:49823000-49833800	Weak transcription	Fetal Brain Male	brain
6	chr13:49823000-49836400	Weak transcription	Colonic Mucosa	Colon
7	chr13:49823000-49837000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr13:49823000-49838000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr13:49823000-49838200	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr13:49823000-49844200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr13:49823200-49833600	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr13:49823200-49833600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr13:49823200-49833600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr13:49823200-49833600	Weak transcription	Fetal Kidney	kidney
15	chr13:49823200-49833600	Weak transcription	Placenta	Placenta
16	chr13:49823400-49833600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr13:49823400-49835000	Weak transcription	Hela-S3	cervix
18	chr13:49823400-49837200	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr13:49823400-49837400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr13:49823400-49837600	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr13:49823400-49844000	Weak transcription	A549	lung
22	chr13:49823600-49833600	Weak transcription	Brain Angular Gyrus	brain
23	chr13:49823600-49833600	Weak transcription	Brain Hippocampus Middle	brain
24	chr13:49823600-49833800	Weak transcription	Colon Smooth Muscle	Colon
25	chr13:49823600-49835200	Weak transcription	K562	blood
26	chr13:49823600-49837400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr13:49823600-49843200	Weak transcription	NHEK	skin
28	chr13:49823800-49855400	Weak transcription	Small Intestine	intestine
29	chr13:49824000-49834600	Weak transcription	Fetal Heart	heart
30	chr13:49824800-49833600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr13:49826400-49833800	Weak transcription	Spleen	Spleen
32	chr13:49826600-49833600	Weak transcription	Gastric	stomach
33	chr13:49826600-49833600	Weak transcription	Pancreas	Pancrea
34	chr13:49826600-49877800	Weak transcription	Psoas Muscle	Psoas
35	chr13:49827600-49837200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
36	chr13:49827800-49832600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr13:49827800-49832800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr13:49827800-49834800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr13:49827800-49837000	Strong transcription	Fetal Muscle Trunk	muscle
40	chr13:49827800-49837800	Strong transcription	Fetal Lung	lung
41	chr13:49827800-49839400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr13:49828800-49832400	Strong transcription	Primary neutrophils fromperipheralblood	blood
43	chr13:49828800-49836600	Strong transcription	Fetal Muscle Leg	muscle
44	chr13:49828800-49837200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
45	chr13:49829200-49835400	Strong transcription	Cortex derived primary cultured neurospheres	brain
46	chr13:49829200-49836000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr13:49829600-49833600	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr13:49829600-49833600	Weak transcription	Aorta	Aorta
49	chr13:49829600-49833600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr13:49829600-49833600	Weak transcription	Fetal Intestine Small	intestine

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