Variant report

Variant	rs12909582
Chromosome Location	chr15:99977186-99977187
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:99974033..99977897-chr15:99978912..99982934,5	K562	blood:
2	chr15:99975615..99977769-chr15:99978276..99979849,2	MCF-7	breast:
3	chr15:99963793..99965594-chr15:99976352..99978718,2	K562	blood:
4	chr15:99976307..99978594-chr15:100018036..100019822,2	MCF-7	breast:
5	chr15:99975316..99977266-chr15:99981293..99982934,2	K562	blood:

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs11247094	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11638998	0.81[EUR][1000 genomes]
rs12050818	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12903392	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1545246	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.80[MEX][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs1561864	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1561866	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1561868	0.84[ASW][hapmap];0.82[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];0.94[TSI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2119939	0.95[ASN][1000 genomes]
rs28393358	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28463528	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2862151	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4965234	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4965235	0.87[ASN][1000 genomes]
rs4965489	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4965490	0.81[ASN][1000 genomes]
rs4965493	0.81[CHB][hapmap];0.96[CHD][hapmap];0.90[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];0.84[EUR][1000 genomes]
rs6598247	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6598248	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6598249	0.81[CHB][hapmap];0.87[JPT][hapmap];0.84[EUR][1000 genomes]
rs7162570	0.80[ASN][1000 genomes]
rs7162817	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7165066	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7167464	0.82[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7169461	0.82[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7169660	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7170529	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7182313	0.91[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8028527	0.85[ASN][1000 genomes]
rs8032786	0.82[EUR][1000 genomes]
rs894416	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:25 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1055008	chr15:99477144-100019861	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv904543	chr15:99513231-99991506	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv533926	chr15:99519820-99997114	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv915926	chr15:99519820-100138705	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
5	nsv817289	chr15:99621061-100138705	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
6	nsv431411	chr15:99621061-100143999	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
7	nsv904546	chr15:99696046-100166300	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
8	nsv1036346	chr15:99752391-100365458	Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
9	nsv542520	chr15:99752391-100365458	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
10	nsv1051560	chr15:99837102-100124483	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
11	nsv817201	chr15:99839238-100537341	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
12	nsv904547	chr15:99940221-99979159	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
13	nsv904548	chr15:99940221-99979418	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
14	nsv904549	chr15:99940221-99991506	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
15	nsv519800	chr15:99950772-99987109	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
16	nsv904550	chr15:99954278-99978524	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
17	nsv904551	chr15:99954278-99979418	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
18	nsv904552	chr15:99954278-99982447	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
19	nsv904553	chr15:99954278-99983175	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
20	nsv904554	chr15:99956954-99979418	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
21	nsv904555	chr15:99956954-99981269	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
22	nsv904556	chr15:99956954-99987109	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
23	nsv904557	chr15:99956954-99991506	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
24	nsv519319	chr15:99972661-99991506	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
25	nsv570728	chr15:99973369-99986764	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12909582	TTC23	cis	parietal	SCAN

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:99971200-99978000	Enhancers	Spleen	Spleen
2	chr15:99971400-99978800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
3	chr15:99971400-99979200	Enhancers	Primary T helper cells fromperipheralblood	blood
4	chr15:99971600-99978800	Enhancers	Primary T cells from cord blood	blood
5	chr15:99972200-99978600	Enhancers	Fetal Thymus	thymus
6	chr15:99972400-99977400	Enhancers	Skeletal Muscle Male	skeletal muscle
7	chr15:99972600-99977400	Enhancers	Placenta Amnion	Placenta Amnion
8	chr15:99972600-99979000	Enhancers	Left Ventricle	heart
9	chr15:99972800-99977800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr15:99972800-99978800	Enhancers	Lung	lung
11	chr15:99972800-99979000	Enhancers	Adipose Nuclei	Adipose
12	chr15:99973400-99978600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
13	chr15:99973800-99978000	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr15:99973800-99978400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
15	chr15:99974000-99977600	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr15:99974000-99977800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr15:99974000-99978200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr15:99974200-99982000	Weak transcription	Gastric	stomach
19	chr15:99974200-99984000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr15:99974400-99977400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr15:99974400-99979000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr15:99974400-99982000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr15:99974600-99977400	Bivalent Enhancer	Fetal Brain Male	brain
24	chr15:99974800-99977600	Weak transcription	NHLF	lung
25	chr15:99974800-99978800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr15:99975000-99979200	Enhancers	Skeletal Muscle Female	skeletal muscle
27	chr15:99975000-99982200	Enhancers	Fetal Heart	heart
28	chr15:99975200-99980000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
29	chr15:99975400-99978800	Enhancers	Right Atrium	heart
30	chr15:99975400-99979000	Enhancers	Right Ventricle	heart
31	chr15:99975800-99977200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr15:99975800-99977200	Weak transcription	Thymus	Thymus
33	chr15:99975800-99977400	Weak transcription	Psoas Muscle	Psoas
34	chr15:99975800-99978000	Weak transcription	HSMMtube	muscle
35	chr15:99975800-99978400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr15:99975800-99978800	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr15:99976000-99977200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr15:99976000-99977600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr15:99976000-99981200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr15:99976000-99982000	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr15:99976000-99982000	Weak transcription	Pancreas	Pancrea
42	chr15:99976000-99982200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr15:99976000-99982200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr15:99976200-99977200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
45	chr15:99976200-99977400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr15:99976200-99977600	Enhancers	Breast Myoepithelial Primary Cells	Breast
47	chr15:99976200-99978000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
48	chr15:99976200-99978200	Weak transcription	NH-A	brain
49	chr15:99976200-99978800	Weak transcription	Fetal Kidney	kidney
50	chr15:99976200-99981400	Weak transcription	Rectal Smooth Muscle	rectum

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