Variant report

Variant	rs3011799
Chromosome Location	chr10:52321618-52321619
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:52321176..52321727-chr10:52383601..52384321,2	MCF-7	breast:
2	chr10:52319465..52323601-chr10:52381894..52385353,11	MCF-7	breast:
3	chr10:52321284..52321942-chr10:52383537..52384335,2	K562	blood:
4	chr10:52321429..52322179-chr10:52412685..52413604,3	K562	blood:
5	chr10:52321608..52322162-chr10:52374026..52374665,2	K562	blood:
6	chr10:52321520..52322241-chr10:52381687..52382340,3	MCF-7	breast:
7	chr10:52321225..52322115-chr10:52384431..52385212,4	K562	blood:
8	chr10:52319643..52322201-chr10:52358538..52360204,2	MCF-7	breast:
9	chr10:52318973..52324648-chr10:52334040..52339164,5	K562	blood:
10	chr10:52313474..52316249-chr10:52319945..52321727,3	K562	blood:
11	chr10:52319893..52329540-chr10:52377624..52388129,20	MCF-7	breast:
12	chr10:52321239..52322152-chr10:52412979..52413544,2	MCF-7	breast:
13	chr10:52321488..52322151-chr10:52374019..52374674,2	MCF-7	breast:
14	chr10:52319647..52323316-chr10:52382184..52387388,6	K562	blood:
15	chr10:52321318..52322646-chr10:52381436..52382589,4	MCF-7	breast:
16	chr10:52176588..52178104-chr10:52321160..52323318,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000198964	Chromatin interaction
ENSG00000226200	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs2208035	1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs2208037	0.81[CEU][hapmap];0.94[YRI][hapmap];0.92[AFR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2339508	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2339509	0.94[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2860490	0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2983348	1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs2983352	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2983358	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2983362	0.86[CEU][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2983363	0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2983365	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2983372	1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs3001855	0.81[YRI][hapmap]
rs3011708	0.90[AFR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3011711	0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3011768	0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs3011778	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3011781	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7094723	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.99[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:97 , 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	chr10:52300800-52322800	Weak transcription	Primary B cells from cord blood	blood
3	chr10:52301600-52327200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr10:52305400-52329600	Weak transcription	Primary T cells fromperipheralblood	blood
5	chr10:52306000-52322000	Weak transcription	Primary T helper cells fromperipheralblood	blood
6	chr10:52306000-52331800	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr10:52308000-52337200	Weak transcription	Primary T cells from cord blood	blood
8	chr10:52310400-52323800	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr10:52310600-52323600	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr10:52310600-52327200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr10:52311000-52323600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr10:52311000-52335800	Weak transcription	Esophagus	oesophagus
13	chr10:52312800-52335800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr10:52312800-52335800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr10:52313000-52322800	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr10:52313200-52333200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr10:52313600-52337400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr10:52315000-52322800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr10:52315000-52329600	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr10:52315200-52323600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr10:52315200-52337400	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr10:52315400-52322000	Weak transcription	Fetal Thymus	thymus
23	chr10:52315600-52323800	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr10:52315600-52336000	Weak transcription	GM12878-XiMat	blood
25	chr10:52316000-52323600	Weak transcription	Fetal Intestine Small	intestine
26	chr10:52316400-52322000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr10:52316400-52322200	Weak transcription	Placenta	Placenta
28	chr10:52316400-52322800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr10:52316400-52323600	Weak transcription	Gastric	stomach
30	chr10:52316400-52325200	Weak transcription	Primary B cells from peripheral blood	blood
31	chr10:52316400-52327200	Weak transcription	Fetal Muscle Leg	muscle
32	chr10:52316400-52331800	Weak transcription	Lung	lung
33	chr10:52316800-52332000	Weak transcription	Aorta	Aorta
34	chr10:52316800-52332600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr10:52318200-52331800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr10:52318400-52323800	Weak transcription	Small Intestine	intestine
37	chr10:52318400-52329600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr10:52319000-52323600	Weak transcription	Left Ventricle	heart
39	chr10:52319200-52335800	Weak transcription	Spleen	Spleen
40	chr10:52319400-52323800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
41	chr10:52319600-52335600	Weak transcription	NHEK	skin
42	chr10:52320200-52322200	Enhancers	NHLF	lung
43	chr10:52320400-52322000	Enhancers	Cortex derived primary cultured neurospheres	brain
44	chr10:52320400-52325400	Enhancers	Liver	Liver
45	chr10:52320600-52321800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr10:52320600-52321800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr10:52320600-52321800	Enhancers	Brain Anterior Caudate	brain
48	chr10:52320600-52321800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
49	chr10:52320600-52321800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
50	chr10:52320600-52321800	Enhancers	Fetal Brain Female	brain

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