Variant report

Variant	rs9349053
Chromosome Location	chr6:38054422-38054423
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10755700	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13198420	0.86[CHB][hapmap]
rs1885325	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1923279	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1979759	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs2201646	0.92[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs259672	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs259675	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs259676	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs259678	0.92[ASW][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs259683	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs259687	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs259693	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4506034	0.82[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs4711522	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4714118	0.81[EUR][1000 genomes]
rs4714123	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4714125	0.82[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs6458040	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6458042	0.94[ASN][1000 genomes]
rs6916091	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6917668	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs6920185	0.81[EUR][1000 genomes]
rs6924634	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6929371	0.92[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[ASN][1000 genomes]
rs6930859	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs6936504	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6938580	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[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7751390	0.80[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs7765798	0.92[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs881681	0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs9369029	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs9369033	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9380716	0.82[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs9394469	0.81[EUR][1000 genomes]
rs9462374	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs9462380	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs9470762	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9470767	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs9470800	0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs9647620	0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028825	chr6:37495154-38278320	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv1017051	chr6:37789341-38084719	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv538203	chr6:37789341-38084719	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1020625	chr6:37833591-38155622	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
5	nsv1021991	chr6:37893949-38738720	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	esv2754649	chr6:37985025-38147910	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
7	nsv885817	chr6:38036420-39019503	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
8	nsv534620	chr6:38049585-38602064	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9349053	LRFN2	cis	parietal	SCAN

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:38017200-38055000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr6:38023000-38054800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr6:38030800-38085800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr6:38031600-38059600	Weak transcription	Spleen	Spleen
5	chr6:38031600-38061600	Weak transcription	Brain Germinal Matrix	brain
6	chr6:38032400-38056200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr6:38033000-38063400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr6:38035000-38084000	Weak transcription	Stomach Smooth Muscle	stomach
9	chr6:38036400-38075000	Weak transcription	Thymus	Thymus
10	chr6:38042800-38060000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr6:38045400-38058800	Weak transcription	Fetal Kidney	kidney
12	chr6:38045600-38055600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr6:38045600-38107000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr6:38045800-38058600	Weak transcription	Fetal Lung	lung
15	chr6:38045800-38059400	Weak transcription	Fetal Heart	heart
16	chr6:38045800-38059600	Weak transcription	Aorta	Aorta
17	chr6:38045800-38079800	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr6:38046000-38084200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr6:38046200-38062600	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr6:38046400-38063200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr6:38046600-38074200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr6:38047000-38062800	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr6:38047200-38058600	Weak transcription	Rectal Smooth Muscle	rectum
24	chr6:38047200-38058600	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr6:38047400-38058800	Weak transcription	Brain Angular Gyrus	brain
26	chr6:38047600-38076200	Weak transcription	Fetal Stomach	stomach
27	chr6:38047800-38055000	Weak transcription	Adipose Nuclei	Adipose
28	chr6:38047800-38057400	Weak transcription	Colon Smooth Muscle	Colon
29	chr6:38047800-38062400	Weak transcription	HepG2	liver
30	chr6:38048000-38060800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr6:38048000-38073000	Weak transcription	Small Intestine	intestine
32	chr6:38048200-38056400	Weak transcription	K562	blood
33	chr6:38048400-38056400	Strong transcription	Primary B cells from cord blood	blood
34	chr6:38048600-38054800	Weak transcription	Colonic Mucosa	Colon
35	chr6:38048800-38055200	Weak transcription	Brain Hippocampus Middle	brain
36	chr6:38048800-38055600	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr6:38048800-38055600	Weak transcription	Brain Substantia Nigra	brain
38	chr6:38049000-38056200	Weak transcription	Brain Anterior Caudate	brain
39	chr6:38049000-38060800	Weak transcription	A549	lung
40	chr6:38049000-38061200	Weak transcription	NHDF-Ad	bronchial
41	chr6:38049200-38058200	Weak transcription	Pancreatic Islets	Pancreatic Islet
42	chr6:38049200-38062200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr6:38049200-38062400	Weak transcription	NHLF	lung
44	chr6:38049200-38062600	Weak transcription	HMEC	breast
45	chr6:38049200-38072600	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr6:38049200-38077400	Weak transcription	Fetal Intestine Small	intestine
47	chr6:38049400-38062400	Weak transcription	Osteobl	bone
48	chr6:38049400-38084400	Weak transcription	Hela-S3	cervix
49	chr6:38049600-38056200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr6:38049800-38055000	Strong transcription	Primary monocytes fromperipheralblood	blood

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