Variant report

Variant	rs10118720
Chromosome Location	chr9:108468886-108468887
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:108456694..108458530-chr9:108468137..108470116,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TAL2-2	chr9:108468659-108469824	NONHSAT133824
2	lnc-TAL2-2	chr9:108468659-108469824	ucscGeneNc_uc004bcy_1

Variant related genes	Relation type
ENSG00000095209	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10115634	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10119254	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10512339	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10733555	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10739209	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10739210	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10739211	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10739212	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10759127	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10759129	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10759131	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10816293	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10978213	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10978216	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2271247	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2271248	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3105993	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3793640	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3794486	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6477461	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7019359	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7026251	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7039618	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7039893	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7859125	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7859253	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7862873	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9299110	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893693	chr9:108427062-108683134	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv615116	chr9:108468129-108546438	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10118720	TMEM38B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:108457800-108472800	Weak transcription	Spleen	Spleen
2	chr9:108457800-108476200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr9:108457800-108492200	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr9:108458000-108472400	Weak transcription	HSMM	muscle
5	chr9:108458000-108473000	Weak transcription	Left Ventricle	heart
6	chr9:108458000-108475200	Weak transcription	Fetal Thymus	thymus
7	chr9:108458000-108475600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr9:108458000-108475600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr9:108458000-108475600	Weak transcription	Thymus	Thymus
10	chr9:108458000-108476000	Weak transcription	Ovary	ovary
11	chr9:108458000-108479200	Weak transcription	Fetal Brain Male	brain
12	chr9:108458000-108497800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr9:108458200-108470600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr9:108458200-108476400	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr9:108458200-108478800	Weak transcription	Brain Hippocampus Middle	brain
16	chr9:108458200-108480800	Weak transcription	Brain Angular Gyrus	brain
17	chr9:108458200-108491400	Weak transcription	HSMMtube	muscle
18	chr9:108458200-108491600	Weak transcription	Brain Anterior Caudate	brain
19	chr9:108458200-108495400	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr9:108458200-108497000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr9:108458400-108470200	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr9:108458400-108470400	Weak transcription	Liver	Liver
23	chr9:108458600-108472600	Weak transcription	Duodenum Mucosa	Duodenum
24	chr9:108458800-108470600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr9:108459000-108476000	Weak transcription	Fetal Brain Female	brain
26	chr9:108459200-108472400	Weak transcription	Dnd41	blood
27	chr9:108459200-108489400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr9:108459600-108470200	Weak transcription	Primary T helper cells PMA-I stimulated	--
29	chr9:108462600-108472600	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr9:108463200-108478400	Weak transcription	Hela-S3	cervix
31	chr9:108463200-108496800	Weak transcription	HepG2	liver
32	chr9:108463400-108487600	Weak transcription	Primary B cells from cord blood	blood
33	chr9:108463800-108470600	Weak transcription	Primary hematopoietic stem cells	blood
34	chr9:108463800-108472400	Weak transcription	K562	blood
35	chr9:108464000-108474800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr9:108464200-108474800	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr9:108464400-108471800	Weak transcription	Psoas Muscle	Psoas
38	chr9:108464400-108476000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr9:108465000-108496600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr9:108465200-108470600	Weak transcription	Primary monocytes fromperipheralblood	blood
41	chr9:108465600-108470400	Weak transcription	GM12878-XiMat	blood
42	chr9:108465600-108476200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr9:108466200-108476200	Weak transcription	Primary T cells fromperipheralblood	blood
44	chr9:108466800-108478400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr9:108467200-108473400	Weak transcription	Primary neutrophils fromperipheralblood	blood
46	chr9:108467600-108470800	Weak transcription	Pancreatic Islets	Pancreatic Islet
47	chr9:108467800-108469000	Strong transcription	Primary B cells from peripheral blood	blood
48	chr9:108467800-108472800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr9:108467800-108474200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr9:108468000-108469400	Strong transcription	Primary hematopoietic stem cells short term culture	blood

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