Variant report

Variant	rs4073852
Chromosome Location	chr1:10045152-10045153
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:10043593..10045454-chr1:10090814..10093281,2	K562	blood:

Variant related genes	Relation type
ENSG00000130939	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10779735	0.90[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs11121508	0.90[AFR][1000 genomes]
rs12026401	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12128632	0.93[AFR][1000 genomes]
rs12128636	0.84[AFR][1000 genomes]
rs1220398	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs1220422	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1237370	0.90[AFR][1000 genomes]
rs12744387	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2380188	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3013785	0.84[AFR][1000 genomes]
rs41280780	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61782860	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61785621	0.92[AFR][1000 genomes]
rs6541074	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6663108	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6673580	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6683452	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72859517	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7522568	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7534615	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9943169	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	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
3	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
4	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
5	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
6	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
7	nsv1001742	chr1:9971776-10116767	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh 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	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4073852	LZIC	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:10021600-10049000	Weak transcription	HSMM	muscle
2	chr1:10025800-10046800	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr1:10028400-10050000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr1:10031600-10045600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr1:10031600-10046200	Strong transcription	Fetal Intestine Small	intestine
6	chr1:10031600-10047200	Strong transcription	Fetal Stomach	stomach
7	chr1:10032000-10045200	Strong transcription	Fetal Muscle Trunk	muscle
8	chr1:10032000-10046600	Strong transcription	Liver	Liver
9	chr1:10032200-10045400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
10	chr1:10032800-10057000	Weak transcription	Psoas Muscle	Psoas
11	chr1:10034400-10048000	Weak transcription	Stomach Mucosa	stomach
12	chr1:10035600-10051800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr1:10036000-10050400	Weak transcription	Primary hematopoietic stem cells	blood
14	chr1:10036600-10047800	Weak transcription	NHEK	skin
15	chr1:10036800-10051200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr1:10037200-10054600	Weak transcription	Fetal Brain Female	brain
17	chr1:10038800-10046000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr1:10039000-10046600	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr1:10039400-10050800	Weak transcription	Colonic Mucosa	Colon
20	chr1:10039600-10048200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr1:10039600-10053600	Weak transcription	Colon Smooth Muscle	Colon
22	chr1:10040000-10045400	Strong transcription	Fetal Muscle Leg	muscle
23	chr1:10040200-10045400	Strong transcription	Skeletal Muscle Female	skeletal muscle
24	chr1:10040400-10046400	Strong transcription	Primary monocytes fromperipheralblood	blood
25	chr1:10041000-10045200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr1:10041000-10045400	Strong transcription	Duodenum Mucosa	Duodenum
27	chr1:10041000-10046000	Strong transcription	Primary neutrophils fromperipheralblood	blood
28	chr1:10041000-10046400	Strong transcription	Rectal Mucosa Donor 29	rectum
29	chr1:10041000-10049200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr1:10042600-10048800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr1:10042600-10050200	Weak transcription	Lung	lung
32	chr1:10042600-10050800	Weak transcription	GM12878-XiMat	blood
33	chr1:10042600-10053800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr1:10042800-10045400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr1:10042800-10045600	Weak transcription	Fetal Lung	lung
36	chr1:10042800-10045800	Weak transcription	NHLF	lung
37	chr1:10042800-10046000	Weak transcription	Primary T helper cells PMA-I stimulated	--
38	chr1:10042800-10046200	Weak transcription	HMEC	breast
39	chr1:10042800-10046600	Weak transcription	Primary T helper cells fromperipheralblood	blood
40	chr1:10042800-10046600	Weak transcription	Aorta	Aorta
41	chr1:10042800-10046800	Weak transcription	Esophagus	oesophagus
42	chr1:10042800-10048600	Weak transcription	Thymus	Thymus
43	chr1:10042800-10049800	Weak transcription	Placenta	Placenta
44	chr1:10042800-10049800	Weak transcription	Right Ventricle	heart
45	chr1:10042800-10050200	Weak transcription	Primary T cells fromperipheralblood	blood
46	chr1:10042800-10050600	Weak transcription	Pancreas	Pancrea
47	chr1:10042800-10050800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
48	chr1:10042800-10051200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr1:10042800-10051200	Weak transcription	HSMMtube	muscle
50	chr1:10042800-10051600	Weak transcription	Fetal Thymus	thymus

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