Variant report

Variant	rs9349017
Chromosome Location	chr6:36811600-36811601
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:36808554..36811671-chr6:36814361..36817752,3	MCF-7	breast:
2	chr6:36811002..36813494-chr6:36814165..36817730,3	MCF-7	breast:
3	chr6:36807425..36809491-chr6:36809760..36812415,2	MCF-7	breast:
4	chr6:36811312..36813099-chr6:36818892..36821190,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CPNE5-1	chr6:36810743-36811911	NONHSAT112234

Variant related genes	Relation type
ENSG00000124772	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11751790	0.86[CHB][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs11754437	0.83[ASN][1000 genomes]
rs11756425	0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs11758600	0.82[ASN][1000 genomes]
rs12661551	0.89[ASN][1000 genomes]
rs12664239	0.87[ASN][1000 genomes]
rs2071822	0.86[CHB][hapmap];0.81[CHD][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs2071823	0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs4711471	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4711472	0.82[ASN][1000 genomes]
rs4714018	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs4714019	0.82[ASN][1000 genomes]
rs4714020	0.85[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs58214515	0.88[EUR][1000 genomes]
rs62406642	0.85[ASN][1000 genomes]
rs62406644	0.89[ASN][1000 genomes]
rs6910582	0.82[ASN][1000 genomes]
rs6910832	0.88[CEU][hapmap];0.87[GIH][hapmap];0.81[TSI][hapmap];0.85[EUR][1000 genomes]
rs6912891	0.87[ASN][1000 genomes]
rs6913047	0.80[ASN][1000 genomes]
rs6934844	0.88[CEU][hapmap];0.87[GIH][hapmap];0.81[TSI][hapmap];0.87[EUR][1000 genomes]
rs72846083	0.82[ASN][1000 genomes]
rs9357229	0.87[ASN][1000 genomes]
rs9357230	0.88[CHD][hapmap];0.89[JPT][hapmap]
rs9366920	0.87[EUR][1000 genomes]
rs9368965	0.85[JPT][hapmap];0.80[ASN][1000 genomes]
rs9380614	0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs9380616	0.92[CEU][hapmap];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023171	chr6:36686935-36880899	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv538202	chr6:36686935-36880899	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv1033261	chr6:36687424-36837315	Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv5262	chr6:36799329-36826210	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats 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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs9349017	LRFN2	cis	cerebellum	SCAN
rs9349017	TCP11	cis	cerebellum	SCAN
rs9349017	SPDEF	cis	parietal	SCAN
rs9349017	PPIL1	Cis_1M	lymphoblastoid	RTeQTL
rs9349017	PNPLA1	cis	parietal	SCAN
rs9349017	SRPK1	cis	cerebellum	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:36808600-36818800	Weak transcription	Dnd41	blood
2	chr6:36808800-36816000	Weak transcription	Spleen	Spleen
3	chr6:36808800-36816600	Weak transcription	Aorta	Aorta
4	chr6:36809000-36812200	Enhancers	Skeletal Muscle Male	skeletal muscle
5	chr6:36809000-36813800	Enhancers	Fetal Muscle Leg	muscle
6	chr6:36809000-36816600	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr6:36809000-36818600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr6:36809000-36820200	Weak transcription	Thymus	Thymus
9	chr6:36809000-36823000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr6:36809200-36812000	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr6:36809200-36812200	Weak transcription	Brain Germinal Matrix	brain
12	chr6:36809200-36812200	Active TSS	Right Atrium	heart
13	chr6:36809200-36812400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr6:36809200-36812400	Weak transcription	Brain Angular Gyrus	brain
15	chr6:36809200-36812600	Weak transcription	Brain Substantia Nigra	brain
16	chr6:36809200-36812600	Weak transcription	Fetal Brain Female	brain
17	chr6:36809200-36816000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr6:36809200-36817000	Weak transcription	Brain Anterior Caudate	brain
19	chr6:36809200-36818000	Weak transcription	HSMM	muscle
20	chr6:36809200-36819200	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr6:36809400-36812000	Weak transcription	HSMMtube	muscle
22	chr6:36809400-36812000	Weak transcription	K562	blood
23	chr6:36809400-36812400	Weak transcription	Brain Cingulate Gyrus	brain
24	chr6:36809400-36812400	Weak transcription	Brain Hippocampus Middle	brain
25	chr6:36809800-36818400	Weak transcription	Colon Smooth Muscle	Colon
26	chr6:36810000-36813000	Enhancers	Fetal Muscle Trunk	muscle
27	chr6:36810400-36812000	Active TSS	Right Ventricle	heart
28	chr6:36810800-36811600	Flanking Active TSS	Left Ventricle	heart
29	chr6:36810800-36812400	Enhancers	Psoas Muscle	Psoas
30	chr6:36810800-36813800	Enhancers	Fetal Heart	heart
31	chr6:36811000-36811600	Enhancers	Stomach Smooth Muscle	stomach
32	chr6:36811000-36815400	Weak transcription	Duodenum Mucosa	Duodenum
33	chr6:36811000-36816000	Weak transcription	Primary monocytes fromperipheralblood	blood
34	chr6:36811000-36816000	Weak transcription	Monocytes-CD14+_RO01746	blood
35	chr6:36811200-36811600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr6:36811200-36811600	Enhancers	Fetal Intestine Small	intestine
37	chr6:36811200-36814000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr6:36811200-36815000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr6:36811400-36811800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr6:36811400-36813200	Enhancers	Skeletal Muscle Female	skeletal muscle
41	chr6:36811400-36823200	Weak transcription	Esophagus	oesophagus
42	chr6:36811600-36811800	Enhancers	Left Ventricle	heart
43	chr6:36811600-36816200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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