Variant report

Variant	rs1372106
Chromosome Location	chr1:9964708-9964709
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:9963862..9967458-chr1:9967663..9970423,5	K562	blood:
2	chr1:9963836..9965578-chr1:9968398..9970356,2	MCF-7	breast:
3	chr1:9958455..9962584-chr1:9963252..9967560,5	MCF-7	breast:
4	chr1:9942309..9944442-chr1:9963388..9967082,3	K562	blood:
5	chr1:9942309..9944442-chr1:9963388..9965697,2	K562	blood:

Variant related genes	Relation type
ENSG00000178585	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1220381	0.84[EUR][1000 genomes]
rs1220382	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1220383	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1220384	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1220391	0.89[ASN][1000 genomes]
rs1220392	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs1220393	0.83[EUR][1000 genomes]
rs1220394	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1220395	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1220396	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs1220404	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1220405	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs1220406	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1220409	1.00[ASN][1000 genomes]
rs1220411	0.87[EUR][1000 genomes]
rs1220412	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs1220413	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1220418	1.00[CEU][hapmap];0.86[YRI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1470160	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1660735	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2083577	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2379108	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2486084	0.92[EUR][1000 genomes]
rs2582980	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2582981	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3120822	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7225	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs935073	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs935074	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs935075	1.00[CEU][hapmap];0.82[YRI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs946275	1.00[CEU][hapmap];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1372106	LZIC	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:9949400-9967600	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr1:9951600-9969000	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr1:9958000-9968800	Weak transcription	Fetal Stomach	stomach
4	chr1:9958800-9969000	Weak transcription	Hela-S3	cervix
5	chr1:9959000-9964800	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr1:9960800-9967800	Weak transcription	Thymus	Thymus
7	chr1:9960800-9969400	Weak transcription	Aorta	Aorta
8	chr1:9961000-9964800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr1:9961000-9965000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr1:9961000-9967600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr1:9961000-9968800	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr1:9961000-9969000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr1:9961000-9969200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr1:9961200-9969000	Weak transcription	Primary T helper cells fromperipheralblood	blood
15	chr1:9961400-9965600	Enhancers	Left Ventricle	heart
16	chr1:9961400-9969000	Weak transcription	Primary B cells from cord blood	blood
17	chr1:9961600-9968800	Weak transcription	Primary hematopoietic stem cells	blood
18	chr1:9961600-9968800	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr1:9961800-9968000	Weak transcription	Primary neutrophils fromperipheralblood	blood
20	chr1:9962000-9965000	Weak transcription	HMEC	breast
21	chr1:9962000-9967600	Weak transcription	Brain Germinal Matrix	brain
22	chr1:9962000-9968800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr1:9962000-9968800	Weak transcription	Small Intestine	intestine
24	chr1:9962000-9969000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr1:9962000-9969000	Weak transcription	Fetal Brain Female	brain
26	chr1:9962200-9964800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr1:9962200-9964800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr1:9962200-9965000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr1:9962200-9965000	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr1:9962200-9966600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr1:9962200-9966600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr1:9962200-9967800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr1:9962200-9967800	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr1:9962200-9968800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr1:9962200-9969000	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr1:9962400-9964800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr1:9962400-9965000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr1:9962400-9965000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr1:9962400-9965000	Weak transcription	K562	blood
40	chr1:9962400-9967600	Weak transcription	Esophagus	oesophagus
41	chr1:9962400-9968800	Weak transcription	Fetal Intestine Small	intestine
42	chr1:9962400-9969000	Weak transcription	Fetal Thymus	thymus
43	chr1:9962400-9969000	Weak transcription	Spleen	Spleen
44	chr1:9962400-9969200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr1:9962600-9966800	Weak transcription	Duodenum Mucosa	Duodenum
46	chr1:9962600-9967400	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr1:9962600-9967600	Weak transcription	Pancreas	Pancrea
48	chr1:9962600-9968800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr1:9962600-9968800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr1:9962600-9969000	Weak transcription	Brain Angular Gyrus	brain

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