Variant report

Variant	rs1972409
Chromosome Location	chr10:6181367-6181368
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:6171306..6174580-chr10:6176089..6182503,5	MCF-7	breast:
2	chr10:6157377..6159891-chr10:6179224..6181720,2	MCF-7	breast:
3	chr10:6180971..6185195-chr10:6203384..6207419,4	MCF-7	breast:
4	chr10:6179137..6182411-chr10:6242546..6245142,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000213994	Chromatin interaction
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]
rs11598494	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1983890	0.97[EUR][1000 genomes]
rs3763700	0.99[AFR][1000 genomes];0.99[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	esv34061	chr10:5726821-6225187	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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
6	nsv894816	chr10:6173416-6190343	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv894817	chr10:6173416-6251252	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer 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	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:6171400-6183200	Weak transcription	Right Atrium	heart
2	chr10:6172200-6182800	Weak transcription	Brain Angular Gyrus	brain
3	chr10:6172400-6181600	Weak transcription	Spleen	Spleen
4	chr10:6172400-6182200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr10:6176600-6185000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr10:6176800-6182000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr10:6177200-6181400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr10:6177200-6181600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr10:6177200-6181800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr10:6177200-6182000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr10:6178200-6182000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr10:6178600-6182000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr10:6179000-6182000	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr10:6179000-6182000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr10:6179000-6182000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr10:6179000-6182400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr10:6179200-6181600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr10:6179200-6182000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr10:6179200-6182200	Weak transcription	HSMM	muscle
20	chr10:6179400-6181600	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr10:6179400-6181800	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr10:6179400-6182000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr10:6179400-6182000	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr10:6179400-6182000	Weak transcription	Adipose Nuclei	Adipose
25	chr10:6179400-6182400	Weak transcription	NHLF	lung
26	chr10:6179400-6182600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr10:6180600-6183400	Weak transcription	Esophagus	oesophagus
28	chr10:6181000-6181600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
29	chr10:6181000-6182200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr10:6181200-6182400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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