Variant report

Variant	rs1220424
Chromosome Location	chr1:10001980-10001981
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr1:10001921-10002020	Lung_OC	lung:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:9991529..9996345-chr1:10001160..10004231,6	K562	blood:
2	chr1:10001502..10006445-chr1:10090966..10096976,9	MCF-7	breast:
3	chr1:9969188..9972816-chr1:10001560..10005397,4	MCF-7	breast:
4	chr1:10001846..10004168-chr1:10458912..10460649,2	K562	blood:
5	chr1:9968043..9973723-chr1:10001891..10008599,10	K562	blood:
6	chr1:9992820..9997928-chr1:9999758..10004449,8	K562	blood:
7	chr1:10001294..10005828-chr1:10093316..10096471,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000228150	TF binding region
NMNAT1	TF binding region
ENSG00000178585	Chromatin interaction
ENSG00000142657	Chromatin interaction
ENSG00000162441	Chromatin interaction
ENSG00000130939	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10779734	0.87[ASN][1000 genomes]
rs11121510	0.85[ASN][1000 genomes]
rs11121512	0.84[ASN][1000 genomes]
rs11828	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12140009	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12140015	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12140058	0.89[ASN][1000 genomes]
rs1220389	0.86[ASN][1000 genomes]
rs1220397	0.83[ASN][1000 genomes]
rs1220399	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1220400	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1220402	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1220420	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1220421	0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1234694	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1237370	0.83[ASN][1000 genomes]
rs1628143	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1660733	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2890358	0.91[ASN][1000 genomes]
rs2919694	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3003377	0.83[ASN][1000 genomes]
rs3003378	0.84[ASN][1000 genomes]
rs3013783	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3013784	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6541073	0.91[ASN][1000 genomes]
rs6661806	0.83[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs6664631	0.86[ASN][1000 genomes]
rs6678023	0.86[ASN][1000 genomes]
rs7517360	0.88[ASN][1000 genomes]
rs7517812	0.84[ASN][1000 genomes]
rs7539191	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	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
6	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
7	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
8	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
9	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
10	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
11	nsv947175	chr1:9996275-10009860	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1220424	LZIC	Cis_1M	lymphoblastoid	RTeQTL
rs1220424	LZIC	cis	multi-tissue	Pritchard

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:9971400-10002000	Weak transcription	Small Intestine	intestine
2	chr1:9972600-10002200	Weak transcription	Right Atrium	heart
3	chr1:9975200-10002600	Weak transcription	Stomach Mucosa	stomach
4	chr1:9983200-10002200	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr1:9983200-10002400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr1:9983600-10002400	Weak transcription	Fetal Heart	heart
7	chr1:9983600-10002400	Weak transcription	Right Ventricle	heart
8	chr1:9984000-10002200	Weak transcription	HMEC	breast
9	chr1:9984600-10002600	Weak transcription	Esophagus	oesophagus
10	chr1:9987000-10002200	Weak transcription	Fetal Brain Male	brain
11	chr1:9987200-10002200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr1:9987400-10002000	Weak transcription	Colonic Mucosa	Colon
13	chr1:9987800-10002200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr1:9988000-10002000	Weak transcription	Rectal Smooth Muscle	rectum
15	chr1:9988200-10002400	Weak transcription	NHLF	lung
16	chr1:9988400-10002000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr1:9988400-10002200	Weak transcription	HUVEC	blood vessel
18	chr1:9989600-10002200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr1:9990200-10002400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr1:9990200-10002400	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr1:9990600-10002200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr1:9990600-10002400	Weak transcription	HSMMtube	muscle
23	chr1:9992200-10002000	Strong transcription	Fetal Intestine Small	intestine
24	chr1:9992200-10002200	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr1:9992200-10002400	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr1:9992200-10002400	Weak transcription	Osteobl	bone
27	chr1:9992400-10002200	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr1:9992400-10002400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr1:9992400-10002600	Weak transcription	Pancreas	Pancrea
30	chr1:9992600-10002600	Weak transcription	Lung	lung
31	chr1:9992800-10002600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr1:9994200-10002600	Weak transcription	Gastric	stomach
33	chr1:9994400-10002600	Weak transcription	Aorta	Aorta
34	chr1:9994600-10002000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr1:9994600-10002400	Weak transcription	Ovary	ovary
36	chr1:9995200-10002200	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr1:9995600-10002000	Weak transcription	Psoas Muscle	Psoas
38	chr1:9995600-10002600	Weak transcription	Spleen	Spleen
39	chr1:9995800-10002200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr1:9995800-10002200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr1:9995800-10002200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr1:9995800-10002400	Weak transcription	A549	lung
43	chr1:9995800-10002400	Weak transcription	NH-A	brain
44	chr1:9996400-10002000	Weak transcription	Colon Smooth Muscle	Colon
45	chr1:9996400-10002200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
46	chr1:9996400-10002200	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr1:9996600-10002000	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr1:9996600-10002000	Weak transcription	Left Ventricle	heart
49	chr1:9996600-10002200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr1:9996600-10002200	Weak transcription	Primary neutrophils fromperipheralblood	blood

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