Variant report

Variant	rs1411408
Chromosome Location	chr9:72437018-72437019
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr9:72436980-72437130	GM12864	blood:	n/a	n/a
2	RAD21	chr9:72437018-72437383	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:72436123..72439031-chr9:72442805..72445416,2	K562	blood:

Variant related genes	Relation type
C9orf135-AS1	TF binding region

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10521434	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11140470	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11140833	1.00[CHB][hapmap]
rs11140836	1.00[CHB][hapmap]
rs11140842	1.00[CHB][hapmap]
rs11140890	1.00[CHB][hapmap]
rs12337927	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12344550	1.00[CHB][hapmap]
rs12347511	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1556208	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17439752	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17517599	0.88[EUR][1000 genomes]
rs17518030	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17518268	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4366141	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7029206	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7036155	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs72723208	0.95[EUR][1000 genomes]
rs72723215	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72723218	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72723219	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72723223	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7854014	1.00[YRI][hapmap]
rs7866489	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv1050920	chr9:72345297-72579301	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv831611	chr9:72361905-72512134	Weak transcription Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv893438	chr9:72363992-72720438	Weak transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:72435400-72437400	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr9:72435400-72437800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr9:72435600-72437400	Enhancers	Fetal Lung	lung
4	chr9:72435800-72437600	Enhancers	Cortex derived primary cultured neurospheres	brain
5	chr9:72435800-72437800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
6	chr9:72436000-72437200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr9:72436000-72437200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr9:72436000-72437600	Enhancers	NHDF-Ad	bronchial
9	chr9:72436000-72438000	Enhancers	Primary T cells from cord blood	blood
10	chr9:72436000-72438400	Weak transcription	K562	blood
11	chr9:72436200-72437800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr9:72436200-72438000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr9:72436200-72440800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr9:72436200-72441200	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr9:72436400-72437400	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
16	chr9:72436400-72437400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr9:72436400-72437400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr9:72436400-72437800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr9:72436400-72437800	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
20	chr9:72436400-72438000	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr9:72436400-72438400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
22	chr9:72436400-72438600	Enhancers	H9 Cell Line	embryonic stem cell
23	chr9:72436400-72439400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
24	chr9:72436600-72437800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr9:72436600-72439400	Enhancers	H1 Cell Line	embryonic stem cell
26	chr9:72436600-72442400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr9:72436800-72437200	Active TSS	iPS-15b Cell Line	embryonic stem cell
28	chr9:72436800-72437400	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
29	chr9:72436800-72437400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr9:72436800-72437600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
31	chr9:72436800-72437800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr9:72437000-72437400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr9:72437000-72437400	Enhancers	Osteobl	bone
34	chr9:72437000-72437800	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
35	chr9:72437000-72437800	Enhancers	Muscle Satellite Cultured Cells	--

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