Variant report

Variant	rs35438121
Chromosome Location	chr9:103204577-103204578
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:103112440..103115986-chr9:103202100..103206037,4	K562	blood:

Variant related genes	Relation type
ENSG00000136891	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs1016176	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1016177	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10989090	0.81[EUR][1000 genomes]
rs10989092	0.81[EUR][1000 genomes]
rs12237166	0.82[EUR][1000 genomes]
rs17740576	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17813447	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17813663	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17813801	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17813854	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2026998	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2151107	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs41274963	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4395949	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56179916	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56313595	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs56720423	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs57241635	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs58030694	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs58698990	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs59668196	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs61306839	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61386923	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7034154	0.80[EUR][1000 genomes]
rs7041933	0.80[EUR][1000 genomes]
rs7046659	0.82[EUR][1000 genomes]
rs72733393	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72733395	0.86[EUR][1000 genomes]
rs72733397	0.85[EUR][1000 genomes]
rs72735110	0.80[EUR][1000 genomes]
rs73655529	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73655530	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73655531	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73655532	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73655533	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73655534	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73655535	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73655536	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73655537	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73655539	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73655540	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73655541	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73655542	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73655543	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73655544	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73655545	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73655546	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73655547	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73655549	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73655550	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73655551	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73655553	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73655554	0.91[AMR][1000 genomes];0.98[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
rs35438121	C9orf30	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:108 , 50 per page) page: 1 2 3

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	chr9:103190800-103206000	Weak transcription	Primary T cells from cord blood	blood
6	chr9:103190800-103206800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr9:103190800-103207200	Weak transcription	Fetal Lung	lung
8	chr9:103190800-103213200	Weak transcription	Primary hematopoietic stem cells	blood
9	chr9:103190800-103217600	Weak transcription	Fetal Intestine Large	intestine
10	chr9:103191000-103206600	Weak transcription	Colonic Mucosa	Colon
11	chr9:103191200-103214200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr9:103191600-103206600	Weak transcription	Aorta	Aorta
13	chr9:103191600-103209200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr9:103191600-103209200	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr9:103191600-103212800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr9:103191600-103213000	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr9:103191600-103214400	Weak transcription	Esophagus	oesophagus
18	chr9:103191800-103206000	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr9:103191800-103206000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr9:103191800-103206000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr9:103191800-103217600	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr9:103191800-103228000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr9:103192000-103206200	Weak transcription	Brain Angular Gyrus	brain
24	chr9:103192000-103206400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr9:103192000-103206400	Weak transcription	Brain Anterior Caudate	brain
26	chr9:103192000-103206600	Weak transcription	Brain Cingulate Gyrus	brain
27	chr9:103192000-103208000	Weak transcription	Brain Substantia Nigra	brain
28	chr9:103192000-103214000	Weak transcription	Colon Smooth Muscle	Colon
29	chr9:103192200-103210600	Weak transcription	Stomach Smooth Muscle	stomach
30	chr9:103192600-103213200	Weak transcription	Fetal Brain Male	brain
31	chr9:103193000-103214400	Weak transcription	Pancreas	Pancrea
32	chr9:103194600-103213200	Weak transcription	Lung	lung
33	chr9:103195000-103205800	Weak transcription	HMEC	breast
34	chr9:103196200-103226400	Weak transcription	Psoas Muscle	Psoas
35	chr9:103197200-103211600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
36	chr9:103197400-103206000	Weak transcription	Fetal Heart	heart
37	chr9:103198400-103210400	Weak transcription	GM12878-XiMat	blood
38	chr9:103198600-103205800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr9:103199800-103208400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr9:103200000-103217000	Weak transcription	K562	blood
41	chr9:103200600-103206200	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr9:103201000-103206400	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr9:103201000-103208200	Weak transcription	Brain Hippocampus Middle	brain
44	chr9:103201200-103215600	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr9:103201600-103215400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr9:103201800-103205800	Weak transcription	Liver	Liver
47	chr9:103202000-103204800	Enhancers	Placenta	Placenta
48	chr9:103202000-103213400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr9:103202000-103215800	Weak transcription	Fetal Thymus	thymus
50	chr9:103202600-103206200	Weak transcription	Small Intestine	intestine

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