Variant report

Variant	rs12261465
Chromosome Location	chr10:52323795-52323796
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:52321910..52324715-chr10:52371827..52374232,3	K562	blood:
2	chr10:52322894..52324648-chr10:52337430..52339164,2	K562	blood:
3	chr10:52318973..52324648-chr10:52334040..52339164,5	K562	blood:
4	chr10:52319893..52329540-chr10:52377624..52388129,20	MCF-7	breast:
5	chr10:52323633..52328946-chr10:52382781..52388541,7	K562	blood:

Variant related genes	Relation type
ENSG00000198964	Chromatin interaction
ENSG00000226200	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10218880	1.00[CEU][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10218927	1.00[CEU][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1028534	1.00[CEU][hapmap]
rs11006161	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11006168	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11006177	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11006224	1.00[CEU][hapmap];0.88[YRI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12241613	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12243444	1.00[CEU][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12262564	1.00[CEU][hapmap];0.94[YRI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12569801	1.00[CEU][hapmap]
rs12569909	1.00[CEU][hapmap]
rs12573520	1.00[CEU][hapmap]
rs16937491	1.00[CEU][hapmap]
rs16937722	0.92[YRI][hapmap]
rs16937771	1.00[CEU][hapmap];0.94[YRI][hapmap]
rs16937775	1.00[CEU][hapmap];0.88[YRI][hapmap]
rs16937786	1.00[CEU][hapmap];0.94[YRI][hapmap]
rs16937874	1.00[CEU][hapmap];0.94[YRI][hapmap];1.00[EUR][1000 genomes]
rs3739990	1.00[CEU][hapmap]
rs41427847	1.00[CEU][hapmap];0.94[YRI][hapmap]
rs56808429	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58158894	1.00[ASN][1000 genomes]
rs58493447	1.00[EUR][1000 genomes]
rs61595381	1.00[EUR][1000 genomes]
rs66936815	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67025766	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67114363	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67414877	1.00[EUR][1000 genomes]
rs72803714	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7911643	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv1054775	chr10:51595893-52392361	Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv1051087	chr10:51886486-52447295	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv916214	chr10:51886486-52458983	Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv918212	chr10:51886486-52465482	Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv817412	chr10:51911034-52432990	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
6	nsv469522	chr10:52276564-52447589	Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
7	nsv482564	chr10:52276564-52447589	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:52280200-52328000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr10:52301600-52327200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr10:52305400-52329600	Weak transcription	Primary T cells fromperipheralblood	blood
4	chr10:52306000-52331800	Weak transcription	Primary T helper cells PMA-I stimulated	--
5	chr10:52308000-52337200	Weak transcription	Primary T cells from cord blood	blood
6	chr10:52310400-52323800	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr10:52310600-52327200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr10:52311000-52335800	Weak transcription	Esophagus	oesophagus
9	chr10:52312800-52335800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr10:52312800-52335800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr10:52313200-52333200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr10:52313600-52337400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr10:52315000-52329600	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr10:52315200-52337400	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr10:52315600-52323800	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr10:52315600-52336000	Weak transcription	GM12878-XiMat	blood
17	chr10:52316400-52325200	Weak transcription	Primary B cells from peripheral blood	blood
18	chr10:52316400-52327200	Weak transcription	Fetal Muscle Leg	muscle
19	chr10:52316400-52331800	Weak transcription	Lung	lung
20	chr10:52316800-52332000	Weak transcription	Aorta	Aorta
21	chr10:52316800-52332600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr10:52318200-52331800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr10:52318400-52323800	Weak transcription	Small Intestine	intestine
24	chr10:52318400-52329600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr10:52319200-52335800	Weak transcription	Spleen	Spleen
26	chr10:52319400-52323800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr10:52319600-52335600	Weak transcription	NHEK	skin
28	chr10:52320400-52325400	Enhancers	Liver	Liver
29	chr10:52321200-52325200	Weak transcription	Right Ventricle	heart
30	chr10:52321400-52324600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr10:52321400-52326000	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr10:52321600-52323800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr10:52321600-52325200	Weak transcription	Brain Substantia Nigra	brain
34	chr10:52321600-52325800	Weak transcription	HMEC	breast
35	chr10:52321600-52327200	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr10:52321600-52335600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr10:52321800-52325400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr10:52321800-52325400	Weak transcription	Ovary	ovary
39	chr10:52321800-52325400	Weak transcription	Right Atrium	heart
40	chr10:52321800-52325600	Weak transcription	Brain Anterior Caudate	brain
41	chr10:52321800-52326600	Weak transcription	Fetal Brain Female	brain
42	chr10:52321800-52327200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr10:52321800-52327200	Weak transcription	Brain Germinal Matrix	brain
44	chr10:52321800-52327200	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr10:52321800-52331600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr10:52321800-52331600	Weak transcription	Psoas Muscle	Psoas
47	chr10:52321800-52335600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr10:52321800-52335600	Weak transcription	Adipose Nuclei	Adipose
49	chr10:52322000-52323800	Weak transcription	HUES64 Cell Line	embryonic stem cell
50	chr10:52322000-52323800	Weak transcription	Brain Angular Gyrus	brain

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