Variant report

Variant	rs61785619
Chromosome Location	chr1:9985693-9985694
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:9983752..9986427-chr1:10003479..10005012,2	K562	blood:

Variant related genes	Relation type
ENSG00000173614	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11828	0.83[ASN][1000 genomes]
rs12140009	0.82[ASN][1000 genomes]
rs12140015	0.82[ASN][1000 genomes]
rs1220398	0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1220399	0.82[ASN][1000 genomes]
rs1237370	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1628143	0.82[ASN][1000 genomes]
rs3013784	0.82[ASN][1000 genomes]
rs3013785	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34851031	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6663108	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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
9	nsv534854	chr1:9964726-10001012	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
10	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
11	nsv1005461	chr1:9972921-10038862	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases
12	nsv534855	chr1:9972921-10038862	Active TSS Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs61785619	LZIC	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:9971400-9987400	Weak transcription	Fetal Stomach	stomach
2	chr1:9971400-9993600	Weak transcription	Aorta	Aorta
3	chr1:9971400-10002000	Weak transcription	Small Intestine	intestine
4	chr1:9971600-9988600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr1:9971600-9991200	Weak transcription	NHEK	skin
6	chr1:9971800-9986600	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr1:9971800-9987000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr1:9971800-9987600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr1:9971800-9989000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr1:9971800-9991800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr1:9972600-9988000	Weak transcription	Lung	lung
12	chr1:9972600-9988600	Weak transcription	Monocytes-CD14+_RO01746	blood
13	chr1:9972600-10002200	Weak transcription	Right Atrium	heart
14	chr1:9972800-9989600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr1:9973000-9988400	Weak transcription	Duodenum Mucosa	Duodenum
16	chr1:9975200-10002600	Weak transcription	Stomach Mucosa	stomach
17	chr1:9977000-9991800	Weak transcription	Brain Germinal Matrix	brain
18	chr1:9978200-9990200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr1:9980200-9988400	Weak transcription	Brain Hippocampus Middle	brain
20	chr1:9980400-9990200	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr1:9980800-9988600	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr1:9981000-9989400	Weak transcription	Left Ventricle	heart
23	chr1:9982000-9986600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr1:9982000-9987400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr1:9982000-9987800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr1:9982000-9987800	Weak transcription	Liver	Liver
27	chr1:9982400-9988400	Weak transcription	Fetal Muscle Leg	muscle
28	chr1:9982800-9987400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr1:9982800-9988200	Weak transcription	Brain Angular Gyrus	brain
30	chr1:9982800-9988600	Weak transcription	K562	blood
31	chr1:9982800-9989600	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr1:9983000-9986400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr1:9983000-9989000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
34	chr1:9983200-9986200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr1:9983200-9986400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr1:9983200-9986400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr1:9983200-9986600	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr1:9983200-9987000	Weak transcription	Fetal Brain Female	brain
39	chr1:9983200-9988400	Weak transcription	Ovary	ovary
40	chr1:9983200-9988600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr1:9983200-9989200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr1:9983200-10002200	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr1:9983200-10002400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr1:9983400-9986400	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr1:9983400-9986400	Weak transcription	HUES64 Cell Line	embryonic stem cell
46	chr1:9983400-9986600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr1:9983400-9987800	Weak transcription	Fetal Intestine Large	intestine
48	chr1:9983600-9986400	Weak transcription	Stomach Smooth Muscle	stomach
49	chr1:9983600-9986600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr1:9983600-9986600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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