Variant report

Variant	rs3771900
Chromosome Location	chr2:152349394-152349395
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	chr2:152347893..152350567-chr2:152361417..152364168,2	K562	blood:

Variant related genes	Relation type
ENSG00000183091	Chromatin interaction
ENSG00000080345	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10182296	0.85[ASN][1000 genomes]
rs10187997	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10432479	0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1065177	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10930688	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13002073	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13391309	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13425109	0.83[EUR][1000 genomes]
rs2123465	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2288195	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2288198	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2432936	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2432938	1.00[ASN][1000 genomes]
rs2432940	0.80[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs2432941	0.90[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2432944	0.87[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs2432951	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2444257	0.91[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2444259	0.96[ASN][1000 genomes]
rs2444260	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2444262	0.89[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2444263	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2444266	0.86[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs2444270	0.87[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs2444272	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2444274	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3815851	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs3815852	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4233649	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4233650	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4233651	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4315520	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4474880	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4664055	0.81[ASN][1000 genomes]
rs4664455	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4994327	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6414089	0.83[EUR][1000 genomes]
rs6433481	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6433482	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6704618	0.82[EUR][1000 genomes]
rs6715917	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6719297	0.88[ASN][1000 genomes]
rs6725513	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6735678	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6744470	0.83[EUR][1000 genomes]
rs7419956	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7558940	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7563568	0.81[ASN][1000 genomes]
rs7566225	0.92[AFR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7575451	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7585717	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9287981	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9287982	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013484	chr2:152028515-152473913	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv535983	chr2:152028515-152473913	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers 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 miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1012139	chr2:152114637-152389516	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv1011339	chr2:152114637-152392940	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv999748	chr2:152135514-152476396	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
6	nsv834418	chr2:152205803-152385516	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
7	nsv933869	chr2:152308156-152391576	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv934136	chr2:152308156-152664443	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
9	nsv437298	chr2:152320118-152356361	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	esv3693428	chr2:152320932-152434896	Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3771900	RIF1	cis	Artery Tibial	GTEx
rs3771900	RIF1	cis	Skin Sun Exposed Lower leg	GTEx
rs3771900	RIF1	Cis_1M	lymphoblastoid	RTeQTL
rs3771900	RIF1	cis	Esophagus Muscularis	GTEx

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:152267600-152379400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr2:152304800-152354000	Weak transcription	Spleen	Spleen
3	chr2:152314000-152349400	Weak transcription	Pancreas	Pancrea
4	chr2:152320800-152358600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr2:152324200-152382400	Weak transcription	Aorta	Aorta
6	chr2:152326400-152367400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr2:152332000-152350400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr2:152332400-152350800	Weak transcription	NHDF-Ad	bronchial
9	chr2:152334000-152349400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr2:152335200-152349400	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr2:152336800-152355000	Strong transcription	Fetal Muscle Leg	muscle
12	chr2:152338200-152356600	Strong transcription	HSMMtube	muscle
13	chr2:152338200-152370000	Strong transcription	Skeletal Muscle Male	skeletal muscle
14	chr2:152338600-152358200	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr2:152339400-152350800	Weak transcription	A549	lung
16	chr2:152339600-152354400	Weak transcription	Primary hematopoietic stem cells	blood
17	chr2:152339800-152350400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr2:152340400-152349800	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr2:152340400-152350000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr2:152340400-152371000	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr2:152340600-152364600	Weak transcription	HepG2	liver
22	chr2:152341200-152366200	Weak transcription	Primary T cells fromperipheralblood	blood
23	chr2:152341400-152350200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr2:152341600-152353400	Weak transcription	NHEK	skin
25	chr2:152341600-152390600	Weak transcription	Left Ventricle	heart
26	chr2:152341800-152350000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr2:152341800-152350400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr2:152341800-152350800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr2:152341800-152364400	Weak transcription	Fetal Intestine Small	intestine
30	chr2:152342200-152355000	Weak transcription	Primary monocytes fromperipheralblood	blood
31	chr2:152342400-152353000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr2:152342600-152349800	Weak transcription	Duodenum Mucosa	Duodenum
33	chr2:152342600-152350200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr2:152342600-152352600	Weak transcription	Lung	lung
35	chr2:152342800-152349800	Weak transcription	Osteobl	bone
36	chr2:152342800-152350600	Weak transcription	Fetal Thymus	thymus
37	chr2:152342800-152366200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr2:152343000-152360800	Weak transcription	Psoas Muscle	Psoas
39	chr2:152343000-152365200	Weak transcription	Fetal Lung	lung
40	chr2:152343200-152422200	Weak transcription	Primary B cells from cord blood	blood
41	chr2:152343400-152355000	Weak transcription	Primary T helper cells fromperipheralblood	blood
42	chr2:152343400-152366800	Weak transcription	Dnd41	blood
43	chr2:152343400-152371000	Weak transcription	Adipose Nuclei	Adipose
44	chr2:152343400-152373000	Weak transcription	Monocytes-CD14+_RO01746	blood
45	chr2:152343600-152362400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr2:152344000-152366400	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr2:152345000-152352800	Strong transcription	Fetal Muscle Trunk	muscle
48	chr2:152346200-152370000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr2:152347000-152387200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr2:152347200-152349400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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