Variant report

Variant	rs9973700
Chromosome Location	chr2:47297973-47297974
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:47296882..47300780-chr2:47402133..47404640,4	K562	blood:
2	chr2:47295023..47298657-chr2:47300855..47310213,9	MCF-7	breast:
3	chr2:47295441..47298329-chr2:47298635..47300784,3	MCF-7	breast:
4	chr2:47293721..47296795-chr2:47297396..47301843,4	K562	blood:
5	chr2:47271650..47273427-chr2:47295265..47298001,2	MCF-7	breast:
6	chr2:47296939..47299679-chr2:47400831..47403571,2	MCF-7	breast:
7	chr2:47297108..47300673-chr2:47304396..47307131,4	K562	blood:

Variant related genes	Relation type
ENSG00000143933	Chromatin interaction
ENSG00000225187	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11125114	0.96[GIH][hapmap];0.81[TSI][hapmap]
rs12465751	0.80[GIH][hapmap];0.90[JPT][hapmap];0.94[TSI][hapmap];0.83[ASN][1000 genomes]
rs13393256	0.81[TSI][hapmap]
rs2347603	0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs2436767	0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs2570515	0.88[CHD][hapmap];0.85[GIH][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs2692220	0.90[JPT][hapmap]
rs7569495	0.81[CEU][hapmap];0.90[MEX][hapmap]
rs7605122	0.88[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7609058	0.88[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][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	nsv817517	chr2:46819371-47715140	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
2	nsv457352	chr2:47004788-47325973	Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv581749	chr2:47004788-47325973	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv1004828	chr2:47056849-47814482	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
5	nsv524970	chr2:47162739-47302095	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	nsv1000377	chr2:47189386-47344029	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	nsv525197	chr2:47210747-47297973	Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv984437	chr2:47270533-47307361	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
9	nsv873998	chr2:47273732-47313624	Enhancers Flanking Active TSS Strong transcription Genic enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9973700	LOC388946	cis	cerebellum	SCAN
rs9973700	SOCS5	cis	parietal	SCAN
rs9973700	DYNC2LI1	cis	cerebellum	SCAN
rs9973700	MAP3K5	trans	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47230200-47302800	Strong transcription	Dnd41	blood
2	chr2:47284600-47298400	Strong transcription	Thymus	Thymus
3	chr2:47288000-47300400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr2:47290400-47299000	Genic enhancers	Fetal Muscle Leg	muscle
5	chr2:47291600-47300800	Weak transcription	Brain Germinal Matrix	brain
6	chr2:47291800-47301200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
7	chr2:47292000-47298800	Enhancers	Placenta	Placenta
8	chr2:47292200-47298200	Weak transcription	Primary neutrophils fromperipheralblood	blood
9	chr2:47292400-47299600	Enhancers	HUVEC	blood vessel
10	chr2:47292600-47302200	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr2:47292800-47300000	Enhancers	NHDF-Ad	bronchial
12	chr2:47293000-47300600	Enhancers	Right Ventricle	heart
13	chr2:47293000-47301400	Enhancers	Skeletal Muscle Female	skeletal muscle
14	chr2:47293200-47299200	Enhancers	Liver	Liver
15	chr2:47294200-47298000	Enhancers	Pancreas	Pancrea
16	chr2:47294200-47298200	Genic enhancers	NHLF	lung
17	chr2:47294400-47298600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
18	chr2:47294400-47301000	Enhancers	Right Atrium	heart
19	chr2:47294600-47300000	Enhancers	Brain Substantia Nigra	brain
20	chr2:47295000-47299200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
21	chr2:47295000-47299200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
22	chr2:47295000-47299200	Enhancers	Psoas Muscle	Psoas
23	chr2:47295000-47299200	Enhancers	Rectal Mucosa Donor 31	rectum
24	chr2:47295000-47300000	Enhancers	Fetal Muscle Trunk	muscle
25	chr2:47295000-47300600	Enhancers	Primary hematopoietic stem cells	blood
26	chr2:47295000-47300600	Genic enhancers	Fetal Stomach	stomach
27	chr2:47295000-47300600	Enhancers	Ovary	ovary
28	chr2:47295000-47300600	Enhancers	NH-A	brain
29	chr2:47295000-47301200	Enhancers	Left Ventricle	heart
30	chr2:47295000-47301400	Genic enhancers	Esophagus	oesophagus
31	chr2:47295200-47298800	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
32	chr2:47295200-47299200	Enhancers	Brain Cingulate Gyrus	brain
33	chr2:47295400-47298000	Enhancers	Primary T helper cells fromperipheralblood	blood
34	chr2:47295400-47298400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
35	chr2:47295400-47298400	Enhancers	Brain Hippocampus Middle	brain
36	chr2:47295400-47298800	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
37	chr2:47295400-47299000	Enhancers	Primary T helper cells PMA-I stimulated	--
38	chr2:47295400-47299200	Enhancers	Primary T helper naive cells from peripheral blood	blood
39	chr2:47295400-47299600	Enhancers	Placenta Amnion	Placenta Amnion
40	chr2:47295400-47300200	Enhancers	Rectal Mucosa Donor 29	rectum
41	chr2:47295400-47301000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr2:47295600-47298000	Enhancers	Duodenum Mucosa	Duodenum
43	chr2:47295600-47299000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
44	chr2:47295600-47299200	Enhancers	Fetal Lung	lung
45	chr2:47295800-47298000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
46	chr2:47295800-47300200	Genic enhancers	Fetal Intestine Small	intestine
47	chr2:47295800-47300200	Enhancers	Lung	lung
48	chr2:47295800-47301200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr2:47295800-47301200	Enhancers	Brain Inferior Temporal Lobe	brain
50	chr2:47296000-47298800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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