Variant report

Variant	rs11140198
Chromosome Location	chr9:86266143-86266144
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:86263153..86266168-chr9:86268070..86271813,4	K562	blood:
2	chr9:86265306..86267714-chr9:86322135..86323961,2	MCF-7	breast:
3	chr9:86264014..86266194-chr9:86272774..86275597,2	MCF-7	breast:
4	chr9:86257425..86259233-chr9:86266050..86268167,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000135018	Chromatin interaction
ENSG00000254473	Chromatin interaction

Extended variants
information (count: 98 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs10115799	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs10119344	0.85[CHB][hapmap]
rs10125432	0.85[CHB][hapmap]
rs1035274	0.85[CHB][hapmap]
rs1044175	0.85[CHB][hapmap]
rs10512136	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[YRI][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10512137	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1056073	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10746717	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10746718	0.85[CHB][hapmap]
rs10746719	0.84[CHB][hapmap]
rs10746720	0.85[CHB][hapmap]
rs10746721	0.85[CHB][hapmap]
rs10780616	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10780617	0.92[AMR][1000 genomes]
rs10780618	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[AMR][1000 genomes]
rs10780619	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10780620	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10780621	0.85[CHB][hapmap]
rs10780622	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10780623	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10780624	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10780625	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10868035	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10868036	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10868037	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10868038	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10868040	0.85[CHB][hapmap]
rs10868042	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10868043	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10868044	0.84[CHB][hapmap]
rs10868045	0.85[CHB][hapmap]
rs11140202	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11140209	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11140212	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11140221	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11140223	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11791175	1.00[CHB][hapmap];0.88[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1333861	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1333862	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1333863	0.85[CHB][hapmap]
rs1333865	0.85[CHB][hapmap]
rs1413293	0.85[CHB][hapmap]
rs1537502	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[YRI][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1537503	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes]
rs1572135	0.85[CHB][hapmap]
rs17080575	0.87[MEX][hapmap]
rs1889260	0.85[CHB][hapmap]
rs1961941	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2058912	0.85[CHB][hapmap]
rs2282220	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2542776	0.85[CHB][hapmap]
rs2780969	0.85[CHB][hapmap]
rs2780972	0.85[CHB][hapmap]
rs2780995	0.85[CHB][hapmap]
rs2781003	0.85[CHB][hapmap]
rs2811909	0.85[CHB][hapmap]
rs2811912	0.85[CHB][hapmap]
rs2811917	0.81[LWK][hapmap]
rs2811921	0.85[CHB][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs2811923	0.85[CHB][hapmap]
rs2811926	0.85[CHB][hapmap]
rs2811927	0.91[CHB][hapmap]
rs2811928	0.85[CHB][hapmap]
rs2811929	0.85[CHB][hapmap]
rs2811930	0.85[CHB][hapmap]
rs2811931	0.83[CHB][hapmap]
rs3750409	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3750410	0.95[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes]
rs3814505	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3814507	0.88[MEX][hapmap]
rs4146740	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4146741	0.85[CHB][hapmap]
rs4242623	0.85[CHB][hapmap]
rs4454364	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4877790	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4877791	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4877793	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4877794	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4877796	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4877797	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4877799	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4877800	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6559737	0.85[CHB][hapmap]
rs7023082	0.85[CHB][hapmap]
rs7039019	0.85[CHB][hapmap]
rs7046388	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72618136	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7860614	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7863266	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7865296	0.85[CHB][hapmap]
rs7866234	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap];0.96[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7871055	0.90[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes]
rs7874980	0.85[CHB][hapmap]
rs868917	1.00[CEU][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs961807	0.85[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893512	chr9:86022215-86323309	Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers 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	29 gene(s)	inside rSNPs	diseases
2	nsv1044639	chr9:86252505-86412041	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11140198	RP11-522I20.3	cis	Whole Blood	GTEx
rs11140198	RP11-522I20.3	cis	Muscle Skeletal	GTEx
rs11140198	UBQLN1	cis	lymphoblastoid	seeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:86239400-86266200	Weak transcription	Colon Smooth Muscle	Colon
2	chr9:86239400-86266400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr9:86239600-86266600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr9:86239600-86272200	Weak transcription	Rectal Smooth Muscle	rectum
5	chr9:86239800-86266800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr9:86243200-86269600	Weak transcription	Pancreas	Pancrea
7	chr9:86243600-86266200	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr9:86244800-86278800	Weak transcription	Spleen	Spleen
9	chr9:86244800-86285800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr9:86245000-86268800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr9:86245200-86266400	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr9:86246000-86266400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr9:86248400-86266200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr9:86252000-86266800	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr9:86252800-86294000	Weak transcription	Small Intestine	intestine
16	chr9:86253000-86268600	Weak transcription	HepG2	liver
17	chr9:86257000-86266800	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr9:86257400-86266400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr9:86257600-86271800	Weak transcription	Colonic Mucosa	Colon
20	chr9:86258400-86266400	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr9:86258600-86271800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr9:86258800-86272600	Weak transcription	Stomach Mucosa	stomach
23	chr9:86259000-86266400	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr9:86259400-86267200	Weak transcription	Hela-S3	cervix
25	chr9:86260200-86266800	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr9:86260200-86267600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr9:86260600-86300400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr9:86260800-86281400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr9:86261000-86280200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr9:86261200-86266400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr9:86261600-86267400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr9:86262400-86266200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
33	chr9:86262400-86266400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr9:86262800-86266400	Weak transcription	Primary T cells fromperipheralblood	blood
35	chr9:86262800-86272000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr9:86263200-86266400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr9:86263400-86266800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr9:86263400-86298800	Strong transcription	Fetal Thymus	thymus
39	chr9:86263600-86268800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr9:86263800-86266600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr9:86264200-86268400	Strong transcription	Muscle Satellite Cultured Cells	--
42	chr9:86264400-86266600	Strong transcription	Fetal Stomach	stomach
43	chr9:86264400-86267600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr9:86264400-86280200	Strong transcription	Fetal Muscle Leg	muscle
45	chr9:86264600-86266600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
46	chr9:86264600-86266600	Strong transcription	Fetal Brain Female	brain
47	chr9:86264600-86267600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr9:86264600-86267800	Strong transcription	NHLF	lung
49	chr9:86264600-86268000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr9:86264600-86268000	Strong transcription	Brain Anterior Caudate	brain

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