Variant report

Variant	rs1016177
Chromosome Location	chr9:103199965-103199966
allele	A/C
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	POLR2A	chr9:103199538-103199969	A549	lung:	n/a	n/a
2	CTCF	chr9:103199820-103199970	BE2_C	brain:	n/a	n/a
3	CTCF	chr9:103199955-103200663	SK-N-SH	brain:	n/a	chr9:103200320-103200341 chr9:103200327-103200340 chr9:103200326-103200342 chr9:103200325-103200343 chr9:103200332-103200339
4	SMC3	chr9:103199632-103200657	SK-N-SH	brain:	n/a	chr9:103200327-103200341
5	RAD21	chr9:103199961-103200722	SK-N-SH	brain:	n/a	chr9:103200332-103200341 chr9:103200327-103200341 chr9:103200323-103200342
6	MYC	chr9:103199879-103200492	MCF10A-Er-Src	breast:	n/a	chr9:103200274-103200284
7	CTCF	chr9:103199903-103200771	A549	lung:	n/a	chr9:103200320-103200341 chr9:103200327-103200340 chr9:103200326-103200342 chr9:103200325-103200343 chr9:103200332-103200339

No.	Distal block	Cell Line	Cell type
1	chr9:103197970..103201753-chr9:103212860..103216897,4	K562	blood:
2	chr9:103198603..103202424-chr9:103204469..103207359,3	K562	blood:
3	chr9:103199462..103202264-chr9:103213712..103215287,2	MCF-7	breast:
4	chr9:103199955..103200924-chr9:103231541..103232083,2	K562	blood:

Variant related genes	Relation type
TMEFF1	TF binding region
MSANTD3	TF binding region
MSANTD3-TMEFF1	TF binding region
ENSG00000241697	Chromatin interaction
ENSG00000251349	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs1016176	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10989090	0.82[EUR][1000 genomes]
rs10989092	0.82[EUR][1000 genomes]
rs12237166	0.81[EUR][1000 genomes]
rs17740576	1.00[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17813447	1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17813663	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17813801	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17813854	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2026998	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2151107	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35438121	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs41274963	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4395949	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs56179916	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56313595	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56720423	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs57241635	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58030694	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58698990	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs59668196	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61306839	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61386923	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7046659	0.81[EUR][1000 genomes]
rs72733393	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72733395	0.87[EUR][1000 genomes]
rs72733397	0.86[EUR][1000 genomes]
rs72735110	0.81[EUR][1000 genomes]
rs73655529	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73655530	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73655531	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73655532	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73655533	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73655534	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73655535	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73655536	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73655537	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73655539	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73655540	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73655541	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73655542	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73655543	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73655544	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73655545	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73655546	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73655547	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73655549	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73655550	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73655551	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73655553	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73655554	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][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	nsv893623	chr9:102648036-103405197	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv825012	chr9:103152205-103256281	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv614955	chr9:103181596-103261227	ZNF genes & repeats Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1016177	C9orf30	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:103190400-103206000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr9:103190400-103214200	Weak transcription	Thymus	Thymus
3	chr9:103190600-103214400	Weak transcription	Primary B cells from cord blood	blood
4	chr9:103190600-103224600	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr9:103190800-103200400	Weak transcription	Liver	Liver
6	chr9:103190800-103204000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr9:103190800-103204400	Weak transcription	Primary B cells from peripheral blood	blood
8	chr9:103190800-103206000	Weak transcription	Primary T cells from cord blood	blood
9	chr9:103190800-103206800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr9:103190800-103207200	Weak transcription	Fetal Lung	lung
11	chr9:103190800-103213200	Weak transcription	Primary hematopoietic stem cells	blood
12	chr9:103190800-103217600	Weak transcription	Fetal Intestine Large	intestine
13	chr9:103191000-103203400	Weak transcription	Fetal Muscle Trunk	muscle
14	chr9:103191000-103206600	Weak transcription	Colonic Mucosa	Colon
15	chr9:103191200-103204200	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr9:103191200-103214200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr9:103191600-103201200	Weak transcription	Fetal Muscle Leg	muscle
18	chr9:103191600-103202000	Weak transcription	Placenta	Placenta
19	chr9:103191600-103202400	Weak transcription	Small Intestine	intestine
20	chr9:103191600-103204200	Weak transcription	Ovary	ovary
21	chr9:103191600-103204400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr9:103191600-103204400	Weak transcription	Primary T helper cells fromperipheralblood	blood
23	chr9:103191600-103204400	Weak transcription	Gastric	stomach
24	chr9:103191600-103206600	Weak transcription	Aorta	Aorta
25	chr9:103191600-103209200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr9:103191600-103209200	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr9:103191600-103212800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr9:103191600-103213000	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr9:103191600-103214400	Weak transcription	Esophagus	oesophagus
30	chr9:103191800-103202200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr9:103191800-103204200	Weak transcription	Primary T helper cells PMA-I stimulated	--
32	chr9:103191800-103204200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr9:103191800-103204200	Weak transcription	Fetal Stomach	stomach
34	chr9:103191800-103206000	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr9:103191800-103206000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr9:103191800-103206000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr9:103191800-103217600	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr9:103191800-103228000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr9:103192000-103200400	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr9:103192000-103200400	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr9:103192000-103204400	Weak transcription	Fetal Brain Female	brain
42	chr9:103192000-103206200	Weak transcription	Brain Angular Gyrus	brain
43	chr9:103192000-103206400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr9:103192000-103206400	Weak transcription	Brain Anterior Caudate	brain
45	chr9:103192000-103206600	Weak transcription	Brain Cingulate Gyrus	brain
46	chr9:103192000-103208000	Weak transcription	Brain Substantia Nigra	brain
47	chr9:103192000-103214000	Weak transcription	Colon Smooth Muscle	Colon
48	chr9:103192200-103204400	Weak transcription	Left Ventricle	heart
49	chr9:103192200-103210600	Weak transcription	Stomach Smooth Muscle	stomach
50	chr9:103192600-103200400	Weak transcription	Brain Hippocampus Middle	brain

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