Variant report

Variant	rs2460558
Chromosome Location	chr10:43856211-43856212
allele	C/T
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:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:43845683..43851518-chr10:43853877..43859694,14	MCF-7	breast:
2	chr10:43851891..43853491-chr10:43856042..43858143,2	MCF-7	breast:
3	chr10:43855555..43859405-chr10:43889416..43893889,5	MCF-7	breast:
4	chr10:43854173..43856222-chr10:43890034..43892908,2	MCF-7	breast:
5	chr10:43853906..43856900-chr10:43857802..43860629,2	MCF-7	breast:
6	chr10:43811335..43814194-chr10:43855788..43859216,3	MCF-7	breast:
7	chr10:43843670..43847999-chr10:43855800..43861023,11	MCF-7	breast:
8	chr10:43571829..43574685-chr10:43855832..43858827,2	MCF-7	breast:
9	chr10:43855373..43860700-chr10:43866814..43875446,19	MCF-7	breast:
10	chr10:43855397..43862555-chr10:43901834..43907536,13	MCF-7	breast:
11	chr10:43855647..43857752-chr10:43878006..43881075,3	MCF-7	breast:
12	chr10:43855385..43857043-chr10:43891115..43893517,2	K562	blood:
13	chr10:43853717..43856256-chr10:43898342..43901234,2	MCF-7	breast:
14	chr10:43853521..43859723-chr10:43870896..43875408,11	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000165731	Chromatin interaction
ENSG00000150201	Chromatin interaction
ENSG00000169813	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10899791	0.81[ASN][1000 genomes]
rs10899792	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10899793	0.81[ASN][1000 genomes]
rs10899794	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10899797	0.90[ASN][1000 genomes]
rs11238526	0.93[ASN][1000 genomes]
rs1126709	0.88[ASN][1000 genomes]
rs12221341	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12257917	0.88[ASN][1000 genomes]
rs17153534	0.81[ASN][1000 genomes]
rs2243492	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2245413	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2245710	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2247979	0.83[ASN][1000 genomes]
rs2247981	0.83[ASN][1000 genomes]
rs2250444	0.80[ASN][1000 genomes]
rs2252800	0.88[ASN][1000 genomes]
rs2255967	0.88[ASN][1000 genomes]
rs2261636	0.80[ASN][1000 genomes]
rs2265887	0.81[ASN][1000 genomes]
rs2265952	0.86[ASN][1000 genomes]
rs2460535	0.96[EUR][1000 genomes]
rs2492407	0.83[ASN][1000 genomes]
rs2493659	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2819032	0.88[ASN][1000 genomes]
rs2819034	0.87[ASN][1000 genomes]
rs2946992	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3000700	0.85[ASN][1000 genomes]
rs4648316	0.81[ASN][1000 genomes]
rs56059584	0.88[ASN][1000 genomes]
rs59383062	0.81[ASN][1000 genomes]
rs60739384	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61859002	0.82[ASN][1000 genomes]
rs7070029	0.83[ASN][1000 genomes]
rs7088430	0.83[ASN][1000 genomes]
rs7905676	0.88[ASN][1000 genomes]
rs7912358	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430159	chr10:43291894-43946294	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription 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 miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
2	nsv916378	chr10:43622151-43868356	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv1043661	chr10:43626619-43890162	Bivalent Enhancer Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription 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	17 gene(s)	inside rSNPs	diseases
4	nsv540574	chr10:43626619-43890162	Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised 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	17 gene(s)	inside rSNPs	diseases
5	nsv1035873	chr10:43721143-43873664	Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv1044422	chr10:43731521-43860307	Bivalent/Poised TSS Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv895087	chr10:43783339-43982390	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
8	nsv831842	chr10:43846541-43987501	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:43844400-43857200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr10:43846600-43857200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr10:43849000-43857000	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr10:43850000-43857000	Weak transcription	Brain Angular Gyrus	brain
5	chr10:43850000-43857000	Weak transcription	Brain Anterior Caudate	brain
6	chr10:43850000-43857000	Weak transcription	Brain Cingulate Gyrus	brain
7	chr10:43851400-43857200	Weak transcription	Brain Substantia Nigra	brain
8	chr10:43851800-43856400	Weak transcription	Primary T helper cells PMA-I stimulated	--
9	chr10:43851800-43856600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr10:43851800-43857000	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr10:43851800-43857000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr10:43851800-43857000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr10:43851800-43857000	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr10:43851800-43857200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr10:43851800-43857200	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr10:43851800-43857200	Weak transcription	HSMMtube	muscle
17	chr10:43852000-43856600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr10:43852000-43856600	Weak transcription	Pancreas	Pancrea
19	chr10:43852000-43857000	Weak transcription	Duodenum Mucosa	Duodenum
20	chr10:43852000-43857000	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr10:43852000-43857200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr10:43852000-43857200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr10:43852000-43857200	Weak transcription	Brain Hippocampus Middle	brain
24	chr10:43852200-43857000	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr10:43852200-43857000	Weak transcription	Fetal Intestine Small	intestine
26	chr10:43852200-43857200	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr10:43852400-43857000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr10:43852400-43857000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr10:43852400-43857000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr10:43852400-43857200	Weak transcription	Stomach Mucosa	stomach
31	chr10:43852400-43857200	Weak transcription	NHEK	skin
32	chr10:43854800-43857000	Weak transcription	Fetal Kidney	kidney
33	chr10:43855200-43856600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr10:43855400-43857000	Weak transcription	HMEC	breast
35	chr10:43855800-43856600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
36	chr10:43856000-43856400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
37	chr10:43856000-43856400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr10:43856000-43856400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr10:43856000-43857000	Weak transcription	Primary hematopoietic stem cells	blood
40	chr10:43856200-43857000	Enhancers	Primary T cells fromperipheralblood	blood

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