Variant report

Variant	rs1220384
Chromosome Location	chr1:9956185-9956186
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1220381	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1220382	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1220392	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1220393	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1220394	0.81[EUR][1000 genomes]
rs1220395	0.81[EUR][1000 genomes]
rs1220396	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1220404	0.82[AMR][1000 genomes]
rs1220405	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1220406	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1220411	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1220412	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1220413	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1220418	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1372106	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1470160	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1660735	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2083577	0.90[EUR][1000 genomes]
rs2379108	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2486084	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2582980	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2582981	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3120822	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7225	0.81[EUR][1000 genomes]
rs935073	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs935074	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs935075	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs946275	0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1220384	LZIC	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:9932600-9960200	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr1:9935600-9960800	Weak transcription	Fetal Intestine Large	intestine
3	chr1:9936400-9960200	Weak transcription	Liver	Liver
4	chr1:9943000-9960200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr1:9943200-9961600	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr1:9943600-9960800	Weak transcription	Primary T cells from cord blood	blood
7	chr1:9949400-9967600	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr1:9950600-9960600	Weak transcription	Brain Germinal Matrix	brain
9	chr1:9951200-9960600	Weak transcription	Colon Smooth Muscle	Colon
10	chr1:9951200-9961600	Weak transcription	Fetal Brain Female	brain
11	chr1:9951400-9962000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr1:9951600-9957600	Weak transcription	Fetal Stomach	stomach
13	chr1:9951600-9960000	Weak transcription	Fetal Heart	heart
14	chr1:9951600-9960200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr1:9951600-9961800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr1:9951600-9969000	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr1:9951800-9960000	Weak transcription	Fetal Muscle Trunk	muscle
18	chr1:9951800-9960400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr1:9951800-9960600	Weak transcription	Stomach Smooth Muscle	stomach
20	chr1:9953000-9960800	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr1:9953200-9959800	Weak transcription	Lung	lung
22	chr1:9953200-9960200	Weak transcription	Fetal Intestine Small	intestine
23	chr1:9953400-9960200	Weak transcription	Esophagus	oesophagus
24	chr1:9953400-9960400	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr1:9953600-9957800	Weak transcription	Left Ventricle	heart
26	chr1:9953600-9960400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr1:9953600-9960400	Weak transcription	Right Ventricle	heart
28	chr1:9953600-9960600	Weak transcription	Fetal Muscle Leg	muscle
29	chr1:9953600-9961200	Weak transcription	Gastric	stomach
30	chr1:9953800-9960000	Weak transcription	Placenta	Placenta
31	chr1:9953800-9960200	Weak transcription	HepG2	liver
32	chr1:9953800-9960600	Weak transcription	Primary B cells from cord blood	blood
33	chr1:9954000-9958600	Weak transcription	HSMMtube	muscle
34	chr1:9954000-9960000	Weak transcription	Fetal Lung	lung
35	chr1:9954000-9964600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr1:9954400-9958400	Weak transcription	Hela-S3	cervix
37	chr1:9954400-9958400	Weak transcription	HSMM	muscle
38	chr1:9954400-9958400	Weak transcription	NH-A	brain
39	chr1:9954400-9958600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr1:9954400-9960000	Weak transcription	Brain Anterior Caudate	brain
41	chr1:9954400-9960000	Weak transcription	Right Atrium	heart
42	chr1:9954400-9960600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr1:9954400-9960600	Weak transcription	Adipose Nuclei	Adipose
44	chr1:9954600-9958600	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr1:9954600-9960200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
46	chr1:9954600-9960200	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr1:9954600-9960400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr1:9954600-9960400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr1:9954600-9960400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr1:9954600-9961400	Weak transcription	Cortex derived primary cultured neurospheres	brain

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