Variant report

Variant	rs1411956
Chromosome Location	chr9:78777937-78777938
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs10781342	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10869713	0.84[ASN][1000 genomes]
rs10869715	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13289256	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1888705	0.88[ASN][1000 genomes]
rs7036047	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831627	chr9:78651134-78817669	Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
2	nsv869152	chr9:78742197-79583399	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv893474	chr9:78753324-78784325	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv893475	chr9:78753324-78817288	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
5	nsv893476	chr9:78768830-78887992	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
6	nsv466422	chr9:78775570-78796522	Strong transcription Genic enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Bivalent Enhancer Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv614691	chr9:78775570-78796522	Genic enhancers Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1411956	TMC1	cis	cerebellum	SCAN
rs1411956	CEP78	cis	cerebellum	SCAN

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:78762800-78780200	Weak transcription	Primary neutrophils fromperipheralblood	blood
2	chr9:78766400-78790000	Weak transcription	Spleen	Spleen
3	chr9:78766600-78785200	Weak transcription	Fetal Kidney	kidney
4	chr9:78770400-78781600	Weak transcription	Brain Substantia Nigra	brain
5	chr9:78770600-78790000	Weak transcription	Brain Hippocampus Middle	brain
6	chr9:78771000-78790000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr9:78771600-78790000	Strong transcription	Duodenum Mucosa	Duodenum
8	chr9:78771800-78778000	Strong transcription	Primary T cells from cord blood	blood
9	chr9:78771800-78778400	Strong transcription	Sigmoid Colon	Sigmoid Colon
10	chr9:78771800-78779600	Strong transcription	Thymus	Thymus
11	chr9:78771800-78779800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr9:78772200-78780000	Strong transcription	Primary T helper cells fromperipheralblood	blood
13	chr9:78772200-78790000	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr9:78772600-78778600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr9:78772600-78779400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
16	chr9:78772600-78790000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr9:78773000-78790000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr9:78773000-78790000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr9:78773200-78778400	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr9:78773200-78778400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr9:78773400-78778400	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr9:78773400-78778400	Strong transcription	Dnd41	blood
23	chr9:78773400-78778800	Strong transcription	Primary T helper cells PMA-I stimulated	--
24	chr9:78773400-78779800	Strong transcription	Monocytes-CD14+_RO01746	blood
25	chr9:78774200-78778200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr9:78774200-78782800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr9:78774200-78785200	Weak transcription	Brain Anterior Caudate	brain
28	chr9:78774400-78778600	Enhancers	Fetal Muscle Leg	muscle
29	chr9:78774400-78784800	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr9:78774400-78790000	Weak transcription	Fetal Brain Male	brain
31	chr9:78774600-78790000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr9:78775200-78785400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr9:78775200-78790000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr9:78775400-78780600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr9:78775400-78789800	Weak transcription	Primary T cells fromperipheralblood	blood
36	chr9:78775400-78790000	Weak transcription	Brain Cingulate Gyrus	brain
37	chr9:78775600-78778200	Strong transcription	Fetal Thymus	thymus
38	chr9:78775600-78778400	Genic enhancers	Fetal Stomach	stomach
39	chr9:78775600-78778600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr9:78775800-78778600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr9:78775800-78778600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr9:78776000-78778000	Enhancers	iPS-15b Cell Line	embryonic stem cell
43	chr9:78776000-78778000	Enhancers	Skeletal Muscle Female	skeletal muscle
44	chr9:78776000-78778000	Enhancers	NHDF-Ad	bronchial
45	chr9:78776000-78778400	Enhancers	NH-A	brain
46	chr9:78776000-78778600	Enhancers	Placenta Amnion	Placenta Amnion
47	chr9:78776000-78778800	Enhancers	HSMM	muscle
48	chr9:78776200-78778400	Enhancers	HUES6 Cell Line	embryonic stem cell
49	chr9:78776200-78778400	Strong transcription	Rectal Mucosa Donor 29	rectum
50	chr9:78776200-78778600	Enhancers	Ovary	ovary

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