Variant report

Variant	rs2248638
Chromosome Location	chr10:43846058-43846059
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:8)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:43845581..43847759-chr10:43871473..43872986,2	MCF-7	breast:
2	chr10:43842351..43846324-chr10:43890114..43894453,4	MCF-7	breast:
3	chr10:43842333..43853034-chr10:43900806..43908178,21	MCF-7	breast:
4	chr10:43844606..43847679-chr10:43848074..43851632,6	MCF-7	breast:
5	chr10:43845449..43848194-chr10:43889287..43891526,2	K562	blood:
6	chr10:43843670..43847999-chr10:43855800..43861023,11	MCF-7	breast:
7	chr10:43844277..43847779-chr10:43901946..43904076,3	MCF-7	breast:
8	chr10:43845683..43851518-chr10:43853877..43859694,14	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FXYD4-2	chr10:43845685-43847096	NONHSAT012954

No data

Variant related genes	Relation type
ENSG00000169813	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs17153617	1.00[CEU][hapmap]
rs17153622	1.00[CEU][hapmap]
rs2248875	0.83[EUR][1000 genomes]
rs2460559	1.00[CEU][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2460562	0.87[AFR][1000 genomes]
rs2493665	1.00[CEU][hapmap];0.89[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3000706	0.93[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs4322345	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55693949	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59307177	0.85[EUR][1000 genomes]
rs7898074	1.00[CEU][hapmap]
rs7922334	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	nsv466882	chr10:43721481-43849358	Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv550697	chr10:43721481-43849358	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	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
9	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

No data

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:43844000-43848600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr10:43844400-43848400	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr10:43844400-43848400	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr10:43844400-43848400	Weak transcription	Hela-S3	cervix
5	chr10:43844400-43848600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr10:43844400-43848600	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr10:43844400-43857200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr10:43844600-43846400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr10:43844600-43848600	Weak transcription	A549	lung
10	chr10:43844600-43849400	Weak transcription	K562	blood
11	chr10:43845000-43846600	Enhancers	Fetal Heart	heart
12	chr10:43845200-43846200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr10:43845400-43846200	Bivalent Enhancer	Fetal Muscle Leg	muscle
14	chr10:43845400-43846400	Bivalent Enhancer	Fetal Lung	lung
15	chr10:43845400-43846400	Bivalent Enhancer	Placenta	Placenta
16	chr10:43845400-43846600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr10:43845600-43846200	Flanking Active TSS	Brain Hippocampus Middle	brain
18	chr10:43845600-43846200	Enhancers	NHEK	skin
19	chr10:43845600-43846600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
20	chr10:43845600-43846600	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
21	chr10:43845600-43846600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
22	chr10:43845600-43846600	Bivalent Enhancer	Stomach Mucosa	stomach
23	chr10:43845800-43846200	Flanking Active TSS	Brain Angular Gyrus	brain
24	chr10:43845800-43846200	Enhancers	Left Ventricle	heart
25	chr10:43845800-43846400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
26	chr10:43845800-43846400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
27	chr10:43845800-43846600	Active TSS	Brain Inferior Temporal Lobe	brain
28	chr10:43845800-43846600	Bivalent Enhancer	Fetal Stomach	stomach
29	chr10:43845800-43846600	Enhancers	Pancreas	Pancrea
30	chr10:43845800-43847000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr10:43846000-43846200	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
32	chr10:43846000-43846200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr10:43846000-43846200	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr10:43846000-43846200	Bivalent/Poised TSS	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr10:43846000-43846200	Flanking Bivalent TSS/Enh	Fetal Kidney	kidney
36	chr10:43846000-43846200	Bivalent Enhancer	Rectal Mucosa Donor 31	rectum
37	chr10:43846000-43846200	Enhancers	Right Ventricle	heart
38	chr10:43846000-43846200	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
39	chr10:43846000-43846400	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr10:43846000-43846400	Enhancers	Right Atrium	heart
41	chr10:43846000-43846400	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
42	chr10:43846000-43846600	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr10:43846000-43846600	Bivalent Enhancer	Primary B cells from peripheral blood	blood
44	chr10:43846000-43846600	Bivalent Enhancer	Primary hematopoietic stem cells	blood
45	chr10:43846000-43846600	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
46	chr10:43846000-43846600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
47	chr10:43846000-43846600	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr10:43846000-43846600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr10:43846000-43846600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr10:43846000-43846600	Active TSS	Brain Anterior Caudate	brain

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