Variant report

Variant	rs9969813
Chromosome Location	chr9:100821624-100821625
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:100820519..100823041-chr9:100848922..100851897,2	K562	blood:
2	chr9:100820689..100822776-chr9:100823410..100826294,2	MCF-7	breast:
3	chr9:100739257..100741486-chr9:100821509..100823548,2	K562	blood:
4	chr9:100742340..100750312-chr9:100816953..100823782,17	MCF-7	breast:
5	chr9:100817802..100822153-chr9:100831375..100837110,8	MCF-7	breast:
6	chr9:100817775..100822653-chr9:100832609..100840095,16	MCF-7	breast:
7	chr9:100743079..100747890-chr9:100817276..100822371,7	K562	blood:

Variant related genes	Relation type
ENSG00000095380	Chromatin interaction
ENSG00000106785	Chromatin interaction
ENSG00000236896	Chromatin interaction
ENSG00000136938	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10124238	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1058446	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10818454	0.94[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.96[ASN][1000 genomes]
rs10818468	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10818472	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.89[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10984977	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12348197	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12349452	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs12685502	0.94[CHD][hapmap];0.81[AMR][1000 genomes]
rs16912590	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28489815	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7855984	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7874696	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9969738	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv482635	chr9:100775549-100953239	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer 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 target site	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9969813	GNRH1	trans	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:100819600-100848400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr9:100820000-100822000	Enhancers	Primary T cells fromperipheralblood	blood
3	chr9:100820000-100822800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr9:100820000-100823000	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr9:100820000-100823000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr9:100820000-100823000	Weak transcription	Brain Cingulate Gyrus	brain
7	chr9:100820000-100823000	Weak transcription	Fetal Muscle Leg	muscle
8	chr9:100820000-100823000	Weak transcription	Left Ventricle	heart
9	chr9:100820000-100823000	Weak transcription	Lung	lung
10	chr9:100820000-100823200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr9:100820000-100823200	Weak transcription	Aorta	Aorta
12	chr9:100820000-100823200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr9:100820000-100823200	Weak transcription	Ovary	ovary
14	chr9:100820000-100824200	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr9:100820000-100826800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr9:100820000-100826800	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr9:100820000-100828400	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr9:100820000-100836400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr9:100820000-100836600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr9:100820000-100836600	Weak transcription	Brain Angular Gyrus	brain
21	chr9:100820000-100843000	Weak transcription	Brain Substantia Nigra	brain
22	chr9:100820000-100843200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr9:100820000-100843200	Weak transcription	Brain Germinal Matrix	brain
24	chr9:100820000-100843200	Weak transcription	Fetal Brain Female	brain
25	chr9:100820000-100847200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr9:100820000-100849600	Weak transcription	Fetal Brain Male	brain
27	chr9:100820000-100850000	Weak transcription	Fetal Kidney	kidney
28	chr9:100820200-100822200	Enhancers	Primary monocytes fromperipheralblood	blood
29	chr9:100820200-100823000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr9:100820200-100823000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr9:100820200-100823000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr9:100820200-100823000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr9:100820200-100823000	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr9:100820200-100823000	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr9:100820200-100823000	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr9:100820200-100823000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr9:100820200-100823000	Weak transcription	Fetal Thymus	thymus
38	chr9:100820200-100823000	Weak transcription	Pancreas	Pancrea
39	chr9:100820200-100823000	Weak transcription	Thymus	Thymus
40	chr9:100820200-100823000	Weak transcription	A549	lung
41	chr9:100820200-100823200	Weak transcription	Right Ventricle	heart
42	chr9:100820200-100824000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr9:100820200-100825800	Weak transcription	Primary B cells from cord blood	blood
44	chr9:100820200-100843000	Weak transcription	Pancreatic Islets	Pancreatic Islet
45	chr9:100820400-100822800	Weak transcription	Fetal Stomach	stomach
46	chr9:100820600-100822400	Enhancers	Stomach Mucosa	stomach
47	chr9:100820600-100822800	Weak transcription	Primary hematopoietic stem cells	blood
48	chr9:100820600-100823000	Weak transcription	Primary B cells from peripheral blood	blood
49	chr9:100820600-100823000	Weak transcription	Fetal Muscle Trunk	muscle
50	chr9:100820600-100824200	Weak transcription	Brain Anterior Caudate	brain

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