Variant report

Variant	rs17711248
Chromosome Location	chr8:10615949-10615950
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:10615706..10617702-chr8:10620374..10622044,2	K562	blood:
2	chr8:10613644..10615982-chr8:10616006..10618005,2	MCF-7	breast:
3	chr8:10615290..10617626-chr8:10678525..10680394,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PINX1-1	chr8:10615296-10618693	NONHSAT125016

Extended variants
information (count: 74 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10503409	0.95[CEU][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap]
rs10503410	0.90[CEU][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1106740	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11776368	1.00[CHD][hapmap]
rs11995539	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11998382	0.85[CEU][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12155811	0.95[CEU][hapmap]
rs12156345	1.00[CHD][hapmap]
rs12375394	0.95[CEU][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap]
rs12750	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1549792	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1549793	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17712981	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17718772	0.90[CEU][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17720365	0.95[CEU][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap]
rs17721089	0.90[CEU][hapmap]
rs17774331	0.95[CEU][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17774398	0.95[CEU][hapmap];1.00[GIH][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17774627	0.95[CEU][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17776404	0.90[CEU][hapmap];0.81[AMR][1000 genomes]
rs17776427	0.95[CEU][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap]
rs17776497	0.95[CEU][hapmap]
rs17776622	0.95[CEU][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap]
rs17776946	0.95[CEU][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap]
rs2005310	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2409654	1.00[CHD][hapmap]
rs2409655	1.00[CHD][hapmap]
rs4240671	1.00[CHD][hapmap]
rs4310166	1.00[CHD][hapmap]
rs4326350	1.00[CHD][hapmap]
rs4841458	1.00[CHD][hapmap]
rs55637012	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs56023918	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56109041	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs56122299	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6984391	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7002757	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7009920	0.95[CEU][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap]
rs714370	0.81[AMR][1000 genomes]
rs73200740	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73200742	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73208756	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73208757	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73208758	0.83[AMR][1000 genomes]
rs73208762	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73208766	0.84[EUR][1000 genomes]
rs73208769	0.81[AMR][1000 genomes]
rs73208773	0.81[AMR][1000 genomes]
rs73208775	0.81[AMR][1000 genomes]
rs73209921	0.81[EUR][1000 genomes]
rs7817252	0.89[CEU][hapmap]
rs7817654	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7826036	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7827063	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7838335	0.95[CEU][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap]
rs891558	1.00[CEU][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs891559	1.00[CEU][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9650658	0.95[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9650659	0.95[CEU][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022994	chr8:10190618-10660122	Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv539466	chr8:10190618-10660122	Enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv917085	chr8:10237508-10828204	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv1022582	chr8:10571218-10636162	Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	nsv539468	chr8:10571218-10636162	Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	nsv1026802	chr8:10576444-10754489	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
7	nsv539469	chr8:10576444-10754489	Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
8	nsv1017836	chr8:10591801-10803617	Enhancers ZNF genes & repeats Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
9	nsv1034988	chr8:10591801-10804243	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
10	nsv519768	chr8:10600254-10691993	Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
11	nsv1024806	chr8:10605438-10662555	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	nsv831232	chr8:10606053-10774948	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
13	nsv1031709	chr8:10610545-10657726	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
14	esv2764105	chr8:10610557-10657726	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
15	nsv519376	chr8:10611708-10691993	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17711248	MFHAS1	cis	cerebellum	SCAN
rs17711248	DEFB136	cis	parietal	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:10609600-10616200	Weak transcription	Primary T cells from cord blood	blood
2	chr8:10610000-10621400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr8:10610600-10620400	Weak transcription	HepG2	liver
4	chr8:10610800-10622200	Weak transcription	Primary B cells from cord blood	blood
5	chr8:10610800-10662000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr8:10611200-10624400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr8:10612600-10617600	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr8:10612600-10621600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr8:10612800-10621600	Weak transcription	Spleen	Spleen
10	chr8:10613200-10622600	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr8:10613400-10621600	Weak transcription	Aorta	Aorta
12	chr8:10613600-10618400	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr8:10613600-10618800	Weak transcription	Fetal Muscle Leg	muscle
14	chr8:10613800-10617800	Weak transcription	Ovary	ovary
15	chr8:10614200-10616600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr8:10614200-10621400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr8:10614400-10634200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr8:10614600-10616600	Weak transcription	K562	blood
19	chr8:10614800-10616000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr8:10614800-10616800	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr8:10614800-10617200	Weak transcription	Esophagus	oesophagus
22	chr8:10614800-10617400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr8:10614800-10617600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr8:10614800-10617600	Weak transcription	HMEC	breast
25	chr8:10614800-10617600	Weak transcription	NHEK	skin
26	chr8:10614800-10617800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr8:10614800-10618400	Weak transcription	Placenta	Placenta
28	chr8:10614800-10618600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr8:10614800-10621400	Weak transcription	Left Ventricle	heart
30	chr8:10614800-10621400	Weak transcription	Lung	lung
31	chr8:10614800-10621800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr8:10614800-10622000	Weak transcription	Hela-S3	cervix
33	chr8:10615000-10621400	Weak transcription	Adipose Nuclei	Adipose
34	chr8:10615200-10618400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr8:10615400-10620800	Weak transcription	Primary T helper cells fromperipheralblood	blood
36	chr8:10615400-10621400	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr8:10615600-10621600	Weak transcription	Dnd41	blood
38	chr8:10615800-10621400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr8:10615800-10621600	Weak transcription	Gastric	stomach

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