Variant report

Variant	rs9919194
Chromosome Location	chr1:10108107-10108108
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:10001503..10004975-chr1:10105430..10108846,3	MCF-7	breast:
2	chr1:10106569..10108860-chr1:10117865..10121125,3	K562	blood:
3	chr1:10106280..10108164-chr1:10128537..10130148,2	K562	blood:
4	chr1:10108005..10110082-chr1:10115252..10117547,2	K562	blood:
5	chr1:10104211..10106912-chr1:10107965..10110739,3	K562	blood:

Variant related genes	Relation type
ENSG00000233623	Chromatin interaction
ENSG00000162441	Chromatin interaction
ENSG00000228150	Chromatin interaction
ENSG00000173614	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10864442	0.80[EUR][1000 genomes]
rs3003376	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs3013788	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs3123522	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs3762290	0.83[AFR][1000 genomes]
rs58528460	0.91[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs61650275	0.82[EUR][1000 genomes]
rs6541075	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6676280	0.86[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs6693449	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7528979	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7539725	0.80[EUR][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	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	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
4	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
5	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
6	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9919194	LZIC	cis	multi-tissue	Pritchard
rs9919194	LZIC	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:10094800-10119400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:10095000-10111400	Weak transcription	GM12878-XiMat	blood
3	chr1:10095000-10115000	Weak transcription	A549	lung
4	chr1:10095000-10115400	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr1:10095000-10116000	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr1:10095000-10116200	Weak transcription	HSMM	muscle
7	chr1:10095000-10127800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr1:10095000-10147600	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr1:10095200-10134400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr1:10095400-10115600	Weak transcription	HUVEC	blood vessel
11	chr1:10098000-10109200	Weak transcription	Dnd41	blood
12	chr1:10098800-10116000	Weak transcription	Hela-S3	cervix
13	chr1:10098800-10131200	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr1:10101800-10113400	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr1:10103000-10116200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr1:10103200-10108800	Weak transcription	Primary B cells from cord blood	blood
17	chr1:10104000-10109400	Weak transcription	Primary neutrophils fromperipheralblood	blood
18	chr1:10104400-10109000	Enhancers	Brain Cingulate Gyrus	brain
19	chr1:10104600-10108200	Enhancers	Brain Angular Gyrus	brain
20	chr1:10104600-10108200	Enhancers	Ovary	ovary
21	chr1:10104600-10108800	Enhancers	Brain Substantia Nigra	brain
22	chr1:10105200-10109400	Enhancers	Left Ventricle	heart
23	chr1:10105200-10113200	Strong transcription	Primary T cells from cord blood	blood
24	chr1:10105400-10109000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr1:10105600-10108400	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr1:10105600-10108600	Weak transcription	Primary monocytes fromperipheralblood	blood
27	chr1:10105600-10110200	Weak transcription	Primary hematopoietic stem cells	blood
28	chr1:10106200-10109000	Genic enhancers	K562	blood
29	chr1:10106400-10108200	Weak transcription	Primary T helper cells PMA-I stimulated	--
30	chr1:10106400-10109200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr1:10106400-10110200	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr1:10106400-10110400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr1:10106400-10111000	Weak transcription	HSMMtube	muscle
34	chr1:10106400-10134000	Weak transcription	Colonic Mucosa	Colon
35	chr1:10106600-10108200	Weak transcription	Duodenum Mucosa	Duodenum
36	chr1:10106600-10110400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr1:10106600-10110400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr1:10106800-10108800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr1:10106800-10109000	Enhancers	Colon Smooth Muscle	Colon
40	chr1:10106800-10109200	Weak transcription	Fetal Muscle Trunk	muscle
41	chr1:10106800-10109400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr1:10106800-10110200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr1:10106800-10115000	Weak transcription	HepG2	liver
44	chr1:10106800-10116600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr1:10106800-10118000	Weak transcription	Fetal Kidney	kidney
46	chr1:10106800-10128400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr1:10106800-10134200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr1:10106800-10155400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
49	chr1:10107000-10108600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr1:10107000-10111000	Weak transcription	Fetal Intestine Large	intestine

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