Variant report

Variant	rs11258515
Chromosome Location	chr10:6445110-6445111
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:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:6274299..6277760-chr10:6442222..6445453,4	MCF-7	breast:
2	chr10:6240172..6247565-chr10:6441706..6450964,34	MCF-7	breast:
3	chr10:6185039..6188332-chr10:6441868..6445811,4	MCF-7	breast:
4	chr10:6336971..6341697-chr10:6441247..6445868,11	MCF-7	breast:
5	chr10:6335347..6345426-chr10:6438966..6446500,25	MCF-7	breast:
6	chr10:6212333..6214108-chr10:6443084..6445414,2	MCF-7	breast:
7	chr10:6149768..6153003-chr10:6443170..6446281,4	MCF-7	breast:
8	chr10:6256631..6260538-chr10:6441320..6445135,3	MCF-7	breast:
9	chr10:6203235..6207397-chr10:6442888..6446681,6	MCF-7	breast:
10	chr10:6241662..6248347-chr10:6438932..6450669,77	MCF-7	breast:
11	chr10:6242432..6246292-chr10:6442347..6445455,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000226705	Chromatin interaction
ENSG00000134453	Chromatin interaction
ENSG00000170525	Chromatin interaction
ENSG00000213994	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10752329	0.90[ASN][1000 genomes]
rs10752330	0.90[ASN][1000 genomes]
rs10906420	0.83[AFR][1000 genomes]
rs10906429	0.89[AFR][1000 genomes]
rs10906504	0.90[ASN][1000 genomes]
rs11258461	0.84[AFR][1000 genomes]
rs11258500	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11258501	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11258589	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11258612	0.92[ASN][1000 genomes]
rs12572911	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17155850	0.88[ASN][1000 genomes]
rs17155855	0.88[ASN][1000 genomes]
rs2296125	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34316142	0.90[ASN][1000 genomes]
rs35935618	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4237436	0.90[ASN][1000 genomes]
rs4750422	0.90[ASN][1000 genomes]
rs590467	0.88[ASN][1000 genomes]
rs681071	0.90[ASN][1000 genomes]
rs686333	0.90[ASN][1000 genomes]
rs71479777	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7898408	0.90[ASN][1000 genomes]
rs961203	0.86[ASN][1000 genomes]
rs9633784	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[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	nsv1042286	chr10:5795129-6578445	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1054044	chr10:6155144-6487217	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	nsv430123	chr10:6309402-6448384	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv430125	chr10:6322167-6477267	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv1053440	chr10:6354798-6669469	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:6433800-6448600	Weak transcription	Primary T cells from cord blood	blood
2	chr10:6442000-6447200	Weak transcription	Spleen	Spleen
3	chr10:6443400-6452000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr10:6443800-6445400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr10:6443800-6446200	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr10:6443800-6451800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr10:6444000-6445400	Enhancers	Brain Hippocampus Middle	brain
8	chr10:6444000-6445600	Weak transcription	Duodenum Mucosa	Duodenum
9	chr10:6444000-6447600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr10:6444000-6447600	Weak transcription	Pancreas	Pancrea
11	chr10:6444000-6447800	Weak transcription	Primary T helper cells PMA-I stimulated	--
12	chr10:6444000-6448200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr10:6444000-6448200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr10:6444000-6451200	Weak transcription	Aorta	Aorta
15	chr10:6444000-6451400	Weak transcription	Rectal Smooth Muscle	rectum
16	chr10:6444000-6451600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr10:6444000-6452000	Weak transcription	Brain Anterior Caudate	brain
18	chr10:6444000-6452000	Weak transcription	Right Ventricle	heart
19	chr10:6444000-6452400	Weak transcription	Right Atrium	heart
20	chr10:6444200-6445200	Enhancers	Brain Substantia Nigra	brain
21	chr10:6444200-6448000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr10:6444200-6448200	Weak transcription	Primary T helper cells fromperipheralblood	blood
23	chr10:6444200-6452000	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr10:6444600-6445200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr10:6444600-6446400	Enhancers	A549	lung
26	chr10:6444600-6447400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr10:6444800-6445600	Enhancers	Skeletal Muscle Male	skeletal muscle
28	chr10:6444800-6446000	Enhancers	Skeletal Muscle Female	skeletal muscle
29	chr10:6445000-6445200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr10:6445000-6445200	Enhancers	Primary hematopoietic stem cells short term culture	blood
31	chr10:6445000-6445200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
32	chr10:6445000-6445200	Enhancers	Dnd41	blood
33	chr10:6445000-6445600	Enhancers	Psoas Muscle	Psoas

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