Variant report

Variant	rs17193990
Chromosome Location	chr21:39867211-39867212
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr21:39866030..39869325-chr21:39869672..39873977,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000157554	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs11909285	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2836457	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2836460	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2836461	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2836462	1.00[EUR][1000 genomes]
rs2836465	1.00[EUR][1000 genomes]
rs2836467	1.00[EUR][1000 genomes]
rs3787908	0.92[CHB][hapmap];0.93[ASN][1000 genomes]
rs6517468	0.85[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1059340	chr21:39817504-39881353	Weak transcription Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv1064436	chr21:39846571-39875576	Active TSS Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	esv1796335	chr21:39866997-39868968	Weak transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:39860400-39879000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr21:39861000-39867600	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr21:39861800-39867600	Weak transcription	Duodenum Mucosa	Duodenum
4	chr21:39862000-39872200	Weak transcription	Gastric	stomach
5	chr21:39862000-39877400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr21:39862200-39871200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr21:39862600-39869400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr21:39865000-39867800	Transcr. at gene 5' and 3'	HUVEC	blood vessel
9	chr21:39865600-39867800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
10	chr21:39865600-39868000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
11	chr21:39865600-39868400	Enhancers	HUES48 Cell Line	embryonic stem cell
12	chr21:39865600-39868400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
13	chr21:39865800-39868400	Flanking Active TSS	Primary hematopoietic stem cells	blood
14	chr21:39865800-39868400	Active TSS	Skeletal Muscle Male	skeletal muscle
15	chr21:39865800-39871000	Active TSS	Adipose Nuclei	Adipose
16	chr21:39866000-39868000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr21:39866000-39868400	Enhancers	HUES6 Cell Line	embryonic stem cell
18	chr21:39866200-39867400	Enhancers	NH-A	brain
19	chr21:39866200-39867600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
20	chr21:39866200-39867800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr21:39866200-39867800	Active TSS	Skeletal Muscle Female	skeletal muscle
22	chr21:39866200-39868000	Active TSS	Lung	lung
23	chr21:39866200-39868200	Enhancers	HUES64 Cell Line	embryonic stem cell
24	chr21:39866200-39868400	Enhancers	ES-I3 Cell Line	embryonic stem cell
25	chr21:39866200-39868400	Enhancers	iPS-20b Cell Line	embryonic stem cell
26	chr21:39866200-39870400	Active TSS	Right Atrium	heart
27	chr21:39866200-39870600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr21:39866600-39867400	Enhancers	Fetal Kidney	kidney
29	chr21:39866600-39867400	Bivalent Enhancer	HSMM	muscle
30	chr21:39866600-39867600	Weak transcription	Brain Anterior Caudate	brain
31	chr21:39866600-39868400	Active TSS	Left Ventricle	heart
32	chr21:39866600-39868400	Active TSS	Right Ventricle	heart
33	chr21:39866600-39868600	Enhancers	iPS-18 Cell Line	embryonic stem cell
34	chr21:39866600-39870200	Active TSS	Psoas Muscle	Psoas
35	chr21:39866800-39867400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
36	chr21:39866800-39867800	Enhancers	iPS-15b Cell Line	embryonic stem cell
37	chr21:39866800-39868000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
38	chr21:39866800-39869400	Weak transcription	Aorta	Aorta
39	chr21:39866800-39869400	Weak transcription	Spleen	Spleen
40	chr21:39866800-39870400	Active TSS	Pancreatic Islets	Pancreatic Islet
41	chr21:39866800-39870400	Active TSS	Fetal Muscle Leg	muscle
42	chr21:39866800-39875200	Weak transcription	HMEC	breast
43	chr21:39867000-39867800	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr21:39867000-39868000	Active TSS	Fetal Muscle Trunk	muscle
45	chr21:39867000-39869200	Weak transcription	Stomach Smooth Muscle	stomach
46	chr21:39867000-39869400	Active TSS	Fetal Thymus	thymus
47	chr21:39867000-39869600	Active TSS	Fetal Adrenal Gland	Adrenal Gland
48	chr21:39867000-39870400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr21:39867000-39878800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr21:39867200-39867400	Enhancers	HSMMtube	muscle

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