Variant report

Variant	rs9982370
Chromosome Location	chr21:39865855-39865856
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr21:39774988..39777692-chr21:39864933..39866829,2	MCF-7	breast:

Extended variants
information (count: 9 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs11700443	0.94[CEU][hapmap];0.83[ASN][1000 genomes]
rs11701364	0.89[JPT][hapmap]
rs2836420	0.87[CEU][hapmap]
rs2836439	0.94[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];0.91[ASN][1000 genomes]
rs2836440	0.91[ASN][1000 genomes]
rs2836444	0.82[CEU][hapmap];0.82[CHD][hapmap];0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs35568883	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

Variant related diseases (count:1)

Disease	PMID	Source
General cognitive ability	25383866	GWAS catalog

Chromatin state (count:53 , 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	chr21:39861200-39866200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr21:39861400-39866200	Weak transcription	NH-A	brain
5	chr21:39861800-39867600	Weak transcription	Duodenum Mucosa	Duodenum
6	chr21:39862000-39866400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr21:39862000-39866600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr21:39862000-39872200	Weak transcription	Gastric	stomach
9	chr21:39862000-39877400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr21:39862200-39866000	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr21:39862200-39871200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr21:39862400-39866800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr21:39862600-39869400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr21:39862800-39866200	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr21:39862800-39866600	Weak transcription	Right Ventricle	heart
16	chr21:39863000-39866200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr21:39863800-39866600	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr21:39864200-39866200	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr21:39864600-39866200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr21:39864800-39866600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr21:39864800-39866800	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
22	chr21:39865000-39867800	Transcr. at gene 5' and 3'	HUVEC	blood vessel
23	chr21:39865200-39866200	Enhancers	Primary B cells from cord blood	blood
24	chr21:39865200-39866200	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr21:39865200-39866800	Enhancers	HSMMtube	muscle
26	chr21:39865200-39867000	Enhancers	Fetal Thymus	thymus
27	chr21:39865600-39866000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
28	chr21:39865600-39866000	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr21:39865600-39866000	Genic enhancers	Aorta	Aorta
30	chr21:39865600-39866200	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr21:39865600-39866200	Transcr. at gene 5' and 3'	Lung	lung
32	chr21:39865600-39866400	Enhancers	Left Ventricle	heart
33	chr21:39865600-39866600	Active TSS	Brain Anterior Caudate	brain
34	chr21:39865600-39866600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
35	chr21:39865600-39866600	Enhancers	HSMM	muscle
36	chr21:39865600-39866800	Enhancers	Primary monocytes fromperipheralblood	blood
37	chr21:39865600-39866800	Enhancers	Fetal Muscle Leg	muscle
38	chr21:39865600-39866800	Enhancers	Spleen	Spleen
39	chr21:39865600-39866800	Enhancers	HMEC	breast
40	chr21:39865600-39867000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
41	chr21:39865600-39867000	Enhancers	Thymus	Thymus
42	chr21:39865600-39867800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
43	chr21:39865600-39868000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
44	chr21:39865600-39868400	Enhancers	HUES48 Cell Line	embryonic stem cell
45	chr21:39865600-39868400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
46	chr21:39865800-39866200	Enhancers	Primary neutrophils fromperipheralblood	blood
47	chr21:39865800-39866200	Weak transcription	Right Atrium	heart
48	chr21:39865800-39866600	Weak transcription	Pancreas	Pancrea
49	chr21:39865800-39867000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr21:39865800-39867000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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