Variant report

Variant	rs61897254
Chromosome Location	chr11:4106495-4106496
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:4105213-4106531	K562	blood:	n/a	n/a
2	POLR2A	chr11:4106415-4106541	HepG2	liver:	n/a	n/a
3	POLR2A	chr11:4105709-4107655	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:3861564..3863892-chr11:4106134..4108924,2	MCF-7	breast:
2	chr11:4104981..4106957-chr11:4107395..4110293,2	K562	blood:

Variant related genes	Relation type
STIM1	TF binding region
ENSG00000167323	Chromatin interaction
ENSG00000177105	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10458900	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10500591	0.80[ASN][1000 genomes]
rs10500592	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10500593	0.82[ASN][1000 genomes]
rs11030286	0.80[ASN][1000 genomes]
rs11030326	0.82[ASN][1000 genomes]
rs11030327	0.81[ASN][1000 genomes]
rs11030417	0.80[ASN][1000 genomes]
rs11030418	0.82[ASN][1000 genomes]
rs11030453	0.81[ASN][1000 genomes]
rs11030478	0.84[ASN][1000 genomes]
rs11030479	0.84[ASN][1000 genomes]
rs11030481	0.84[ASN][1000 genomes]
rs11030484	0.84[ASN][1000 genomes]
rs11030485	0.84[ASN][1000 genomes]
rs11030486	0.84[ASN][1000 genomes]
rs11030697	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11030796	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11525342	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11529865	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12222250	0.80[ASN][1000 genomes]
rs1372803	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16929410	0.92[ASN][1000 genomes]
rs16929438	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16929467	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16929477	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16929480	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16929488	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16929492	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16929529	0.84[ASN][1000 genomes]
rs16929531	0.84[ASN][1000 genomes]
rs16929538	0.84[ASN][1000 genomes]
rs16929542	0.81[ASN][1000 genomes]
rs16929546	0.84[ASN][1000 genomes]
rs16929611	0.81[ASN][1000 genomes]
rs16929616	0.80[ASN][1000 genomes]
rs1822286	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1899478	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2167563	0.80[ASN][1000 genomes]
rs2284448	0.81[ASN][1000 genomes]
rs2284449	0.81[ASN][1000 genomes]
rs3750994	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55679086	0.82[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs55978228	0.84[ASN][1000 genomes]
rs56126231	0.80[ASN][1000 genomes]
rs56140937	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59242983	0.87[ASN][1000 genomes]
rs61897163	0.80[ASN][1000 genomes]
rs61897164	0.80[ASN][1000 genomes]
rs61897166	0.81[ASN][1000 genomes]
rs61897170	0.81[ASN][1000 genomes]
rs61897171	0.81[ASN][1000 genomes]
rs61897194	0.81[ASN][1000 genomes]
rs61897195	0.80[ASN][1000 genomes]
rs61897201	0.81[ASN][1000 genomes]
rs61897202	0.84[ASN][1000 genomes]
rs61897206	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61897234	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61897237	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61897238	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61897257	0.81[ASN][1000 genomes]
rs6578423	0.81[ASN][1000 genomes]
rs72851736	0.84[ASN][1000 genomes]
rs73417150	0.85[AFR][1000 genomes]
rs73431611	0.81[AFR][1000 genomes]
rs750526	0.80[ASN][1000 genomes]
rs7934581	0.99[ASN][1000 genomes]
rs7941743	0.81[ASN][1000 genomes]
rs894454	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv896896	chr11:4010409-4185595	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	esv2758253	chr11:4055945-4510188	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
3	esv2759797	chr11:4055945-4510188	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
4	nsv428248	chr11:4055945-4510188	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
5	nsv832053	chr11:4096527-4330263	Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Enhancers ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:4066400-4107800	Weak transcription	Small Intestine	intestine
2	chr11:4070800-4108600	Weak transcription	HSMM	muscle
3	chr11:4079000-4112600	Weak transcription	Fetal Brain Female	brain
4	chr11:4082600-4107400	Weak transcription	Stomach Mucosa	stomach
5	chr11:4086200-4115200	Weak transcription	NHDF-Ad	bronchial
6	chr11:4087600-4115000	Weak transcription	HSMMtube	muscle
7	chr11:4087800-4107800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr11:4088600-4107800	Weak transcription	Right Ventricle	heart
9	chr11:4091600-4107600	Weak transcription	Psoas Muscle	Psoas
10	chr11:4093600-4112600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr11:4093800-4115000	Weak transcription	Brain Germinal Matrix	brain
12	chr11:4093800-4115200	Weak transcription	Fetal Kidney	kidney
13	chr11:4094000-4107800	Weak transcription	Brain Angular Gyrus	brain
14	chr11:4094000-4108600	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr11:4094000-4108600	Weak transcription	Osteobl	bone
16	chr11:4094000-4115000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr11:4094000-4115000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr11:4094000-4115200	Weak transcription	Brain Substantia Nigra	brain
19	chr11:4095800-4109400	Weak transcription	K562	blood
20	chr11:4096000-4107600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr11:4098200-4115000	Weak transcription	Hela-S3	cervix
22	chr11:4099400-4107800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr11:4099400-4111200	Strong transcription	Fetal Thymus	thymus
24	chr11:4100200-4115200	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr11:4100400-4110400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr11:4100600-4106600	Strong transcription	Monocytes-CD14+_RO01746	blood
27	chr11:4100600-4115200	Weak transcription	NHLF	lung
28	chr11:4101000-4107400	Strong transcription	Primary T cells fromperipheralblood	blood
29	chr11:4101000-4110600	Strong transcription	Primary B cells from peripheral blood	blood
30	chr11:4101400-4108000	Strong transcription	Primary T cells from cord blood	blood
31	chr11:4101400-4112800	Strong transcription	Thymus	Thymus
32	chr11:4101400-4113600	Strong transcription	Primary B cells from cord blood	blood
33	chr11:4101400-4114000	Strong transcription	Primary neutrophils fromperipheralblood	blood
34	chr11:4101400-4114200	Strong transcription	Stomach Smooth Muscle	stomach
35	chr11:4101600-4107000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr11:4101600-4113200	Strong transcription	Dnd41	blood
37	chr11:4101600-4113800	Strong transcription	Adipose Nuclei	Adipose
38	chr11:4101800-4108000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr11:4101800-4108400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr11:4101800-4112000	Strong transcription	Rectal Mucosa Donor 29	rectum
41	chr11:4101800-4113400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr11:4101800-4114000	Strong transcription	Fetal Stomach	stomach
43	chr11:4102000-4107000	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr11:4102000-4108400	Strong transcription	Primary T killer memory cells from peripheral blood	blood
45	chr11:4102000-4113200	Strong transcription	Liver	Liver
46	chr11:4102200-4106600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr11:4102200-4107400	Strong transcription	Primary T helper cells PMA-I stimulated	--
48	chr11:4102200-4107400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr11:4102200-4108000	Strong transcription	Primary T helper cells fromperipheralblood	blood
50	chr11:4102200-4109800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood

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