Variant report

Variant	rs62319574
Chromosome Location	chr4:120392364-120392365
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11724055	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13103899	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13107334	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13116789	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13121569	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13124532	0.84[EUR][1000 genomes]
rs13133969	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13140150	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17358860	0.80[EUR][1000 genomes]
rs2389870	0.80[EUR][1000 genomes]
rs35264119	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35289699	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35985971	0.85[ASN][1000 genomes]
rs3775850	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3775851	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3775856	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs61747388	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62319578	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62319609	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs71614451	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs988146	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[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	nsv916641	chr4:119780023-120777320	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv1012868	chr4:120014630-120464880	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv537232	chr4:120014630-120464880	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
4	nsv879842	chr4:120244085-120424087	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	nsv427694	chr4:120250511-120501728	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv879843	chr4:120326323-120502461	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv879844	chr4:120341296-120449810	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv879846	chr4:120341296-120491714	Weak transcription Strong transcription Genic enhancers Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
9	nsv879845	chr4:120341296-120502461	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
10	nsv879847	chr4:120371729-120450159	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
11	nsv967793	chr4:120386467-120392750	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs62319574	RP11-33B1.1	cis	Heart Left Ventricle	GTEx
rs62319574	RP11-33B1.1	cis	lung	GTEx
rs62319574	LOC645513	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:120376400-120392400	Weak transcription	Fetal Lung	lung
2	chr4:120376400-120471600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr4:120376600-120397200	Weak transcription	Aorta	Aorta
4	chr4:120376600-120399000	Weak transcription	Stomach Mucosa	stomach
5	chr4:120376600-120401200	Weak transcription	Psoas Muscle	Psoas
6	chr4:120376600-120419200	Weak transcription	Brain Cingulate Gyrus	brain
7	chr4:120377000-120416000	Weak transcription	Colon Smooth Muscle	Colon
8	chr4:120377200-120392400	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr4:120377200-120393200	Weak transcription	Primary B cells from cord blood	blood
10	chr4:120377200-120397400	Weak transcription	Lung	lung
11	chr4:120377200-120400000	Weak transcription	Esophagus	oesophagus
12	chr4:120377200-120400600	Weak transcription	A549	lung
13	chr4:120377200-120401000	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr4:120377200-120403400	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr4:120377200-120415600	Weak transcription	Brain Substantia Nigra	brain
16	chr4:120377200-120416200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr4:120377200-120419600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr4:120377200-120433800	Weak transcription	Gastric	stomach
19	chr4:120377400-120392400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr4:120377400-120393200	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr4:120377400-120393400	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr4:120377400-120395000	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr4:120377400-120396400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr4:120377400-120397400	Weak transcription	Thymus	Thymus
25	chr4:120377400-120397400	Weak transcription	Hela-S3	cervix
26	chr4:120377400-120397800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr4:120377400-120398400	Weak transcription	Fetal Intestine Small	intestine
28	chr4:120377400-120399800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr4:120377400-120400200	Weak transcription	Ovary	ovary
30	chr4:120377400-120400400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr4:120377400-120400600	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr4:120377400-120400600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr4:120377400-120401000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr4:120377400-120403000	Weak transcription	Fetal Brain Female	brain
35	chr4:120377400-120415200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
36	chr4:120377400-120416200	Weak transcription	Rectal Smooth Muscle	rectum
37	chr4:120377400-120439000	Weak transcription	Small Intestine	intestine
38	chr4:120377400-120439000	Weak transcription	Spleen	Spleen
39	chr4:120377600-120393400	Weak transcription	Placenta	Placenta
40	chr4:120377600-120394200	Weak transcription	Primary hematopoietic stem cells	blood
41	chr4:120377600-120396800	Weak transcription	HSMMtube	muscle
42	chr4:120377600-120397200	Weak transcription	Brain Angular Gyrus	brain
43	chr4:120377600-120400400	Weak transcription	Brain Germinal Matrix	brain
44	chr4:120377600-120401000	Weak transcription	HMEC	breast
45	chr4:120377600-120402200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr4:120377600-120403000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
47	chr4:120377600-120441000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
48	chr4:120377600-120501200	Weak transcription	Pancreas	Pancrea
49	chr4:120377800-120400800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr4:120383600-120395800	Strong transcription	Dnd41	blood

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