Variant report

Variant	rs56144989
Chromosome Location	chr11:66269965-66269966
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	chr11:66246350..66248077-chr11:66269423..66272131,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000255517	Chromatin interaction
ENSG00000254986	Chromatin interaction

Extended variants
information (count: 96 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs10501397	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10896124	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10896125	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10896129	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11227495	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11227497	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11227498	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11227499	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11227500	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11227501	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11227502	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11227503	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11227506	0.84[ASN][1000 genomes]
rs11227509	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11227510	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11227511	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11227512	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11227514	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11227515	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11227522	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11227523	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11227525	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11227527	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11227534	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11550299	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11821155	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11822028	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11822099	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11824771	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12099041	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12221821	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12223479	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12272545	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17065	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17147644	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17495838	0.81[EUR][1000 genomes]
rs17496250	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17496586	0.94[EUR][1000 genomes]
rs17580784	0.85[EUR][1000 genomes]
rs2075792	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2276406	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2277302	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2279864	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2279865	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2298806	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2305532	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2305533	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2305534	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2305535	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28414721	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3179961	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35733139	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3737525	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3741360	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3816492	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3819247	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3825065	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3892818	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4542420	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4576	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4630309	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4930182	0.85[EUR][1000 genomes]
rs4930183	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4930377	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4930378	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4930379	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4930380	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57045447	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57207756	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57288351	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57596493	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57634456	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57691879	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57724777	0.92[EUR][1000 genomes]
rs59829960	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59982644	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs60358007	0.89[EUR][1000 genomes]
rs60645853	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61561111	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61582507	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7104378	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7116921	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7116940	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7123176	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7928882	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7939759	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7943327	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7950407	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7950790	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]

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	esv3392427	chr11:65981489-66273695	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	118 gene(s)	inside rSNPs	diseases
2	nsv897771	chr11:66011280-66362997	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	124 gene(s)	inside rSNPs	diseases
3	nsv897780	chr11:66083129-66362997	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
4	nsv832193	chr11:66120339-66278805	Strong transcription Bivalent/Poised TSS Weak transcription Active TSS Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
5	nsv468601	chr11:66234023-66296114	Strong transcription Flanking Active TSS Genic enhancers Enhancers Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
6	nsv555224	chr11:66234023-66296114	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
7	nsv522277	chr11:66234023-66493825	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs56144989	CCS	Cis_1M	lymphoblastoid	RTeQTL
rs56144989	DPP3	cis	Thyroid	GTEx
rs56144989	CTD-3074O7.5	cis	Esophagus Mucosa	GTEx
rs56144989	CTD-3074O7.5	cis	Whole Blood	GTEx

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:66248600-66277600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr11:66248600-66277600	Weak transcription	Fetal Brain Male	brain
3	chr11:66248600-66277600	Weak transcription	Fetal Lung	lung
4	chr11:66248600-66278000	Weak transcription	NHDF-Ad	bronchial
5	chr11:66248800-66277600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr11:66248800-66277600	Weak transcription	K562	blood
7	chr11:66249800-66273200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr11:66251200-66277600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr11:66251800-66274600	Strong transcription	Fetal Stomach	stomach
10	chr11:66254400-66272600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr11:66255800-66277800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr11:66259600-66270600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr11:66259600-66277600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr11:66261000-66271800	Weak transcription	Left Ventricle	heart
15	chr11:66261000-66272000	Weak transcription	HUVEC	blood vessel
16	chr11:66261000-66272600	Weak transcription	HSMM	muscle
17	chr11:66261000-66277800	Weak transcription	Psoas Muscle	Psoas
18	chr11:66261200-66271800	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr11:66261200-66272400	Weak transcription	Colon Smooth Muscle	Colon
20	chr11:66261200-66277800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr11:66261200-66278000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr11:66261600-66277600	Weak transcription	Stomach Mucosa	stomach
23	chr11:66261800-66272400	Weak transcription	HepG2	liver
24	chr11:66261800-66277800	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr11:66262400-66277600	Weak transcription	Rectal Smooth Muscle	rectum
26	chr11:66263400-66271800	Weak transcription	Right Ventricle	heart
27	chr11:66263400-66272200	Weak transcription	A549	lung
28	chr11:66263600-66272200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr11:66263600-66272800	Weak transcription	GM12878-XiMat	blood
30	chr11:66263600-66277800	Weak transcription	NH-A	brain
31	chr11:66263800-66271200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr11:66264600-66278000	Weak transcription	HMEC	breast
33	chr11:66264800-66270800	Weak transcription	Primary hematopoietic stem cells	blood
34	chr11:66264800-66277600	Weak transcription	Hela-S3	cervix
35	chr11:66264800-66277800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr11:66264800-66277800	Weak transcription	Osteobl	bone
37	chr11:66265000-66272000	Weak transcription	Ovary	ovary
38	chr11:66265000-66272000	Weak transcription	NHLF	lung
39	chr11:66265000-66272200	Weak transcription	Aorta	Aorta
40	chr11:66265000-66272400	Weak transcription	Brain Angular Gyrus	brain
41	chr11:66265000-66277800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr11:66265200-66270800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr11:66265200-66271400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr11:66265200-66272000	Weak transcription	Colonic Mucosa	Colon
45	chr11:66265200-66272000	Weak transcription	Gastric	stomach
46	chr11:66265200-66272000	Weak transcription	Pancreas	Pancrea
47	chr11:66265200-66272200	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr11:66265200-66272200	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr11:66265200-66272400	Weak transcription	Brain Substantia Nigra	brain
50	chr11:66265200-66277600	Weak transcription	Small Intestine	intestine

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