Variant report

Variant	rs7539725
Chromosome Location	chr1:10125407-10125408
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:10123267..10128743-chr1:10130766..10138737,8	K562	blood:
2	chr1:10118522..10121469-chr1:10124651..10126938,2	K562	blood:
3	chr1:10118522..10121469-chr1:10122769..10126938,6	K562	blood:
4	chr1:9968902..9971327-chr1:10123444..10125645,2	K562	blood:

Variant related genes	Relation type
ENSG00000178585	Chromatin interaction
ENSG00000233623	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs11121516	0.85[ASN][1000 genomes]
rs3003376	0.81[GIH][hapmap]
rs61650275	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6693449	0.80[EUR][1000 genomes]
rs7517812	0.84[CEU][hapmap]
rs7528979	0.85[CEU][hapmap];0.93[GIH][hapmap];0.84[TSI][hapmap]
rs9919194	0.80[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	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
2	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
3	nsv527217	chr1:10093457-10257167	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7539725	LZIC	cis	multi-tissue	Pritchard
rs7539725	KIF1B	cis	parietal	SCAN
rs7539725	LZIC	Cis_1M	lymphoblastoid	RTeQTL
rs7539725	LZIC	cis	lymphoblastoid	seeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:10095000-10127800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:10095000-10147600	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr1:10095200-10134400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr1:10098800-10131200	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr1:10106400-10134000	Weak transcription	Colonic Mucosa	Colon
6	chr1:10106800-10128400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr1:10106800-10134200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr1:10106800-10155400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr1:10107000-10140600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr1:10107400-10135200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr1:10107400-10165400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr1:10109000-10126400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr1:10109400-10158400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr1:10111400-10127000	Weak transcription	Fetal Lung	lung
15	chr1:10113000-10132000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr1:10116600-10145000	Weak transcription	Stomach Mucosa	stomach
17	chr1:10118000-10125600	Weak transcription	HSMM	muscle
18	chr1:10118200-10163000	Weak transcription	Aorta	Aorta
19	chr1:10118400-10127000	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr1:10118600-10126200	Weak transcription	HSMMtube	muscle
21	chr1:10118800-10132000	Weak transcription	Primary T cells from cord blood	blood
22	chr1:10119200-10155200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr1:10119600-10132000	Weak transcription	Primary T cells fromperipheralblood	blood
24	chr1:10119800-10125600	Weak transcription	GM12878-XiMat	blood
25	chr1:10119800-10132200	Weak transcription	Thymus	Thymus
26	chr1:10120000-10125600	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr1:10120000-10128400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr1:10120000-10156400	Weak transcription	Spleen	Spleen
29	chr1:10120000-10162600	Weak transcription	Gastric	stomach
30	chr1:10120200-10128400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr1:10120200-10131800	Weak transcription	Primary B cells from cord blood	blood
32	chr1:10120400-10125600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr1:10120400-10132000	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr1:10120400-10134400	Weak transcription	Dnd41	blood
35	chr1:10120400-10163000	Weak transcription	Fetal Kidney	kidney
36	chr1:10120800-10134200	Weak transcription	Primary B cells from peripheral blood	blood
37	chr1:10121800-10141400	Weak transcription	Hela-S3	cervix
38	chr1:10123600-10127000	Enhancers	Right Ventricle	heart
39	chr1:10123600-10127400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr1:10123800-10126200	Weak transcription	Fetal Stomach	stomach
41	chr1:10123800-10126400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr1:10124000-10125600	Enhancers	Primary hematopoietic stem cells short term culture	blood
43	chr1:10124000-10126600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr1:10124000-10126800	Enhancers	Brain Inferior Temporal Lobe	brain
45	chr1:10124000-10126800	Enhancers	Skeletal Muscle Male	skeletal muscle
46	chr1:10124000-10127000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr1:10124000-10127000	Enhancers	Brain Hippocampus Middle	brain
48	chr1:10124000-10127400	Enhancers	Primary hematopoietic stem cells	blood
49	chr1:10124000-10128000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
50	chr1:10124000-10128000	Enhancers	Psoas Muscle	Psoas

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