Variant report

Variant	rs2379108
Chromosome Location	chr1:9968537-9968538
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:9936836..9938925-chr1:9967640..9970664,3	MCF-7	breast:
2	chr1:9790874..9793270-chr1:9967778..9969493,2	K562	blood:
3	chr1:9927613..9929212-chr1:9967136..9969117,2	K562	blood:
4	chr1:9951877..9955765-chr1:9967549..9972934,5	K562	blood:
5	chr1:9931884..9936639-chr1:9967934..9971147,6	MCF-7	breast:
6	chr1:9968043..9973723-chr1:10001891..10008599,10	K562	blood:
7	chr1:9965103..9967822-chr1:9967870..9969778,4	K562	blood:
8	chr1:9950314..9954439-chr1:9967446..9971626,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000178585	Chromatin interaction
ENSG00000173614	Chromatin interaction
ENSG00000202415	Chromatin interaction
ENSG00000162441	Chromatin interaction
ENSG00000228150	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1220381	0.84[EUR][1000 genomes]
rs1220382	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1220383	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1220384	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1220391	0.93[ASN][1000 genomes]
rs1220392	0.83[EUR][1000 genomes]
rs1220393	0.83[EUR][1000 genomes]
rs1220394	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1220395	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1220396	0.83[EUR][1000 genomes]
rs1220404	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1220405	0.85[EUR][1000 genomes]
rs1220406	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1220409	0.96[ASN][1000 genomes]
rs1220411	0.87[EUR][1000 genomes]
rs1220412	0.87[EUR][1000 genomes]
rs1220413	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1220418	0.88[EUR][1000 genomes]
rs1372106	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1470160	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1660735	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2083577	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2486084	0.92[EUR][1000 genomes]
rs2582980	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2582981	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3120822	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7225	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs935073	0.85[EUR][1000 genomes]
rs935074	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs935075	0.90[EUR][1000 genomes]
rs946275	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3385337	chr1:9105242-10082223	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	549 gene(s)	inside rSNPs	diseases
2	nsv871610	chr1:9655795-10008221	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	esv3417409	chr1:9683992-10241703	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	esv3372906	chr1:9838995-10052992	Genic enhancers Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv545380	chr1:9918183-9987007	Weak transcription Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	nsv1012469	chr1:9925714-10147796	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
7	nsv1012301	chr1:9963962-10118393	Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
8	nsv534853	chr1:9963962-10118393	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
9	nsv534854	chr1:9964726-10001012	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2379108	LZIC	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:9951600-9969000	Weak transcription	HUES48 Cell Line	embryonic stem cell
2	chr1:9958000-9968800	Weak transcription	Fetal Stomach	stomach
3	chr1:9958800-9969000	Weak transcription	Hela-S3	cervix
4	chr1:9960800-9969400	Weak transcription	Aorta	Aorta
5	chr1:9961000-9968800	Weak transcription	Primary T cells fromperipheralblood	blood
6	chr1:9961000-9969000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr1:9961000-9969200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr1:9961200-9969000	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr1:9961400-9969000	Weak transcription	Primary B cells from cord blood	blood
10	chr1:9961600-9968800	Weak transcription	Primary hematopoietic stem cells	blood
11	chr1:9961600-9968800	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr1:9962000-9968800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr1:9962000-9968800	Weak transcription	Small Intestine	intestine
14	chr1:9962000-9969000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr1:9962000-9969000	Weak transcription	Fetal Brain Female	brain
16	chr1:9962200-9968800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr1:9962200-9969000	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr1:9962400-9968800	Weak transcription	Fetal Intestine Small	intestine
19	chr1:9962400-9969000	Weak transcription	Fetal Thymus	thymus
20	chr1:9962400-9969000	Weak transcription	Spleen	Spleen
21	chr1:9962400-9969200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr1:9962600-9968800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr1:9962600-9968800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr1:9962600-9969000	Weak transcription	Brain Angular Gyrus	brain
25	chr1:9962600-9969000	Weak transcription	Fetal Lung	lung
26	chr1:9962800-9968600	Weak transcription	Fetal Brain Male	brain
27	chr1:9962800-9968800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr1:9962800-9968800	Weak transcription	Brain Anterior Caudate	brain
29	chr1:9962800-9968800	Weak transcription	Brain Hippocampus Middle	brain
30	chr1:9962800-9968800	Weak transcription	Stomach Smooth Muscle	stomach
31	chr1:9962800-9969000	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr1:9962800-9969200	Weak transcription	Gastric	stomach
33	chr1:9963600-9968800	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr1:9963600-9969000	Weak transcription	Brain Substantia Nigra	brain
35	chr1:9964400-9968800	Weak transcription	Fetal Heart	heart
36	chr1:9964800-9968800	Weak transcription	Brain Cingulate Gyrus	brain
37	chr1:9965000-9968800	Weak transcription	NHDF-Ad	bronchial
38	chr1:9965200-9968800	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr1:9965400-9968800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr1:9965400-9968800	Weak transcription	GM12878-XiMat	blood
41	chr1:9965400-9968800	Weak transcription	NH-A	brain
42	chr1:9965400-9969000	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr1:9965400-9969000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr1:9965400-9969000	Weak transcription	Osteobl	bone
45	chr1:9965600-9968800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr1:9965600-9968800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr1:9965600-9968800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr1:9965600-9968800	Weak transcription	Placenta	Placenta
49	chr1:9965600-9968800	Weak transcription	Psoas Muscle	Psoas
50	chr1:9965600-9968800	Weak transcription	K562	blood

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