Variant report

Variant	rs59400494
Chromosome Location	chr10:6272571-6272572
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:6236304..6239251-chr10:6270821..6273315,2	MCF-7	breast:
2	chr10:6261699..6263729-chr10:6269817..6272606,2	K562	blood:
3	chr10:6254275..6256496-chr10:6272419..6274768,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000170525	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs17152400	0.83[AFR][1000 genomes]
rs56046905	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74112209	0.86[AFR][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	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	nsv1040721	chr10:6155144-6322566	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv540476	chr10:6155144-6322566	Genic enhancers Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	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
5	nsv1041039	chr10:6217724-6354858	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
6	nsv894836	chr10:6246678-6435374	Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
7	nsv525622	chr10:6251252-6281215	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:6247000-6280600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr10:6247200-6281000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr10:6253200-6278800	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr10:6253400-6276600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr10:6253400-6276800	Strong transcription	Fetal Intestine Small	intestine
6	chr10:6253400-6278400	Strong transcription	Primary T helper cells PMA-I stimulated	--
7	chr10:6253800-6281000	Weak transcription	Stomach Mucosa	stomach
8	chr10:6254000-6273400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr10:6254200-6273800	Strong transcription	Spleen	Spleen
10	chr10:6254400-6279200	Strong transcription	Dnd41	blood
11	chr10:6254600-6275600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr10:6254600-6279200	Strong transcription	Cortex derived primary cultured neurospheres	brain
13	chr10:6254600-6280000	Strong transcription	Primary neutrophils fromperipheralblood	blood
14	chr10:6254800-6277800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr10:6255000-6279200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr10:6255000-6279200	Strong transcription	Fetal Stomach	stomach
17	chr10:6255200-6277000	Strong transcription	Duodenum Smooth Muscle	Duodenum
18	chr10:6255200-6277800	Strong transcription	HUES6 Cell Line	embryonic stem cell
19	chr10:6255200-6279200	Strong transcription	Primary T cells from cord blood	blood
20	chr10:6255200-6279200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
21	chr10:6255200-6279400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr10:6255400-6272600	Strong transcription	H9 Cell Line	embryonic stem cell
23	chr10:6255400-6276600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
24	chr10:6255400-6276600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr10:6255400-6276600	Strong transcription	Brain Cingulate Gyrus	brain
26	chr10:6255400-6276800	Strong transcription	HUES48 Cell Line	embryonic stem cell
27	chr10:6255400-6276800	Strong transcription	Primary T helper cells fromperipheralblood	blood
28	chr10:6255400-6276800	Strong transcription	Duodenum Mucosa	Duodenum
29	chr10:6255400-6277400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr10:6255400-6278400	Strong transcription	Liver	Liver
31	chr10:6255400-6278600	Strong transcription	Primary monocytes fromperipheralblood	blood
32	chr10:6255400-6278800	Strong transcription	HUES64 Cell Line	embryonic stem cell
33	chr10:6255400-6279000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr10:6255400-6279400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr10:6255600-6272600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
36	chr10:6255600-6274000	Strong transcription	Fetal Intestine Large	intestine
37	chr10:6255600-6274400	Strong transcription	Fetal Muscle Leg	muscle
38	chr10:6255600-6274600	Strong transcription	Brain Inferior Temporal Lobe	brain
39	chr10:6255600-6276000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr10:6255600-6276400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr10:6255600-6276400	Strong transcription	Pancreas	Pancrea
42	chr10:6255600-6276600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr10:6255600-6276600	Strong transcription	Rectal Mucosa Donor 29	rectum
44	chr10:6255600-6276600	Strong transcription	Thymus	Thymus
45	chr10:6255600-6277000	Strong transcription	Sigmoid Colon	Sigmoid Colon
46	chr10:6255800-6278800	Strong transcription	Fetal Brain Female	brain
47	chr10:6256200-6279000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr10:6256200-6279200	Strong transcription	Adipose Nuclei	Adipose
49	chr10:6256400-6279200	Strong transcription	Skeletal Muscle Male	skeletal muscle
50	chr10:6256800-6273800	Strong transcription	Brain Hippocampus Middle	brain

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