Variant report

Variant	rs10467975
Chromosome Location	chr15:43097652-43097653
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:43094398..43098116-chr15:43199741..43201552,3	K562	blood:

Variant related genes	Relation type
ENSG00000128881	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs11070380	1.00[CEU][hapmap];0.92[JPT][hapmap];0.90[YRI][hapmap];0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11070382	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.95[YRI][hapmap]
rs11853250	0.93[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.84[TSI][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11854668	0.85[EUR][1000 genomes]
rs12323990	0.85[ASW][hapmap];0.81[LWK][hapmap];0.80[YRI][hapmap]
rs12441352	0.93[ASN][1000 genomes]
rs12591415	1.00[ASW][hapmap];0.80[YRI][hapmap]
rs12592573	0.93[ASW][hapmap];0.85[YRI][hapmap]
rs12594600	1.00[ASW][hapmap];0.90[YRI][hapmap]
rs12594696	1.00[ASW][hapmap];0.80[YRI][hapmap]
rs12594765	0.93[ASW][hapmap];0.85[YRI][hapmap]
rs16957031	0.80[YRI][hapmap]
rs16957037	0.85[ASW][hapmap];0.81[LWK][hapmap];0.80[YRI][hapmap]
rs16957055	0.93[ASW][hapmap];0.86[LWK][hapmap];0.85[YRI][hapmap]
rs16957061	0.93[ASW][hapmap]
rs16957063	0.93[ASW][hapmap];0.84[LWK][hapmap];0.85[YRI][hapmap]
rs16957120	0.80[YRI][hapmap]
rs16957165	0.81[ASW][hapmap];1.00[CEU][hapmap];0.92[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.92[TSI][hapmap];0.85[YRI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs16957167	1.00[CEU][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap];0.89[EUR][1000 genomes]
rs16957244	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[GIH][hapmap];0.92[JPT][hapmap];1.00[LWK][hapmap];0.95[YRI][hapmap]
rs16957250	1.00[CEU][hapmap];0.92[GIH][hapmap];0.92[JPT][hapmap]
rs16957264	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs2682073	0.93[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];0.92[JPT][hapmap];0.90[LWK][hapmap];0.90[YRI][hapmap]
rs3742992	0.85[YRI][hapmap]
rs3742995	0.93[ASW][hapmap];0.84[LWK][hapmap];0.85[YRI][hapmap]
rs3803341	1.00[CEU][hapmap];0.81[GIH][hapmap];0.86[JPT][hapmap]
rs4334272	1.00[ASW][hapmap];0.84[YRI][hapmap]
rs4923955	1.00[CEU][hapmap];0.81[GIH][hapmap]
rs55805543	0.90[ASN][1000 genomes]
rs55927779	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6493065	0.93[ASW][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];0.86[LWK][hapmap];1.00[MKK][hapmap];0.90[YRI][hapmap];0.81[AFR][1000 genomes]
rs67920450	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7174028	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.85[YRI][hapmap]
rs7178567	0.93[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.87[LWK][hapmap];0.80[YRI][hapmap]
rs7181238	0.93[ASW][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];0.85[YRI][hapmap]
rs8028699	0.90[YRI][hapmap]
rs8031767	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[GIH][hapmap];0.92[JPT][hapmap];1.00[LWK][hapmap];0.95[YRI][hapmap]
rs8033336	0.93[ASW][hapmap];0.85[YRI][hapmap]
rs8037022	1.00[CEU][hapmap];0.81[GIH][hapmap];0.86[JPT][hapmap]
rs8042481	1.00[CEU][hapmap];0.81[GIH][hapmap]
rs9920562	0.86[ASW][hapmap];1.00[MKK][hapmap];0.85[YRI][hapmap]
rs9920624	0.94[MKK][hapmap];0.80[YRI][hapmap]
rs9920935	0.86[ASW][hapmap];0.86[LWK][hapmap];1.00[MKK][hapmap];0.85[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv528725	chr15:42755555-43104406	Weak transcription Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv427959	chr15:42931181-43207353	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv977054	chr15:43015821-43171355	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS Active TSS 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	8 gene(s)	inside rSNPs	diseases
4	nsv1050128	chr15:43056145-43262736	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv542368	chr15:43056145-43262736	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv525461	chr15:43062548-43482127	Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
7	nsv904134	chr15:43097652-43357406	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10467975	TTBK2	cis	parietal	SCAN
rs10467975	CCNDBP1	Cis_1M	lymphoblastoid	RTeQTL
rs10467975	ELL3	cis	lymphoblastoid	seeQTL

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:43053600-43112200	Weak transcription	Rectal Smooth Muscle	rectum
2	chr15:43054800-43146000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr15:43056800-43116800	Weak transcription	HepG2	liver
4	chr15:43057600-43107000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr15:43060800-43122200	Weak transcription	GM12878-XiMat	blood
6	chr15:43063400-43136200	Weak transcription	Psoas Muscle	Psoas
7	chr15:43064000-43114200	Weak transcription	Fetal Kidney	kidney
8	chr15:43064800-43150800	Weak transcription	HSMM	muscle
9	chr15:43067400-43147200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr15:43075200-43143800	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr15:43075400-43135800	Weak transcription	HSMMtube	muscle
12	chr15:43075600-43150800	Weak transcription	Colon Smooth Muscle	Colon
13	chr15:43075800-43117200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr15:43075800-43119200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr15:43075800-43124800	Weak transcription	Hela-S3	cervix
16	chr15:43075800-43134800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr15:43075800-43159200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr15:43077400-43102200	Weak transcription	Fetal Brain Male	brain
19	chr15:43089400-43101800	Weak transcription	NH-A	brain
20	chr15:43089400-43104000	Weak transcription	NHDF-Ad	bronchial
21	chr15:43089400-43105800	Weak transcription	Osteobl	bone
22	chr15:43089600-43118400	Weak transcription	HMEC	breast
23	chr15:43089800-43102400	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr15:43089800-43165200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr15:43091400-43103000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr15:43091800-43135400	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr15:43092400-43097800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr15:43092600-43098000	Strong transcription	Monocytes-CD14+_RO01746	blood
29	chr15:43092600-43098600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr15:43092600-43105000	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr15:43092800-43098000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr15:43093000-43111800	Weak transcription	Fetal Heart	heart
33	chr15:43093000-43124600	Weak transcription	Small Intestine	intestine
34	chr15:43093400-43099000	Strong transcription	Primary T cells from cord blood	blood
35	chr15:43093600-43098200	Strong transcription	Left Ventricle	heart
36	chr15:43094200-43101800	Weak transcription	Primary B cells from cord blood	blood
37	chr15:43094200-43101800	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr15:43094400-43104400	Weak transcription	NHLF	lung
39	chr15:43094400-43118000	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr15:43094400-43118000	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr15:43094400-43163800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr15:43094600-43099200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr15:43094600-43100200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr15:43094600-43101800	Weak transcription	Brain Anterior Caudate	brain
45	chr15:43094600-43102000	Weak transcription	Brain Substantia Nigra	brain
46	chr15:43094600-43102400	Weak transcription	Brain Germinal Matrix	brain
47	chr15:43094600-43102400	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr15:43094600-43111400	Weak transcription	Pancreas	Pancrea
49	chr15:43094600-43115800	Weak transcription	Colonic Mucosa	Colon
50	chr15:43094600-43150800	Weak transcription	Aorta	Aorta

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