Variant report

Variant	rs1047957
Chromosome Location	chr2:152333773-152333774
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:152333590..152335850-chr2:152341846..152344009,2	K562	blood:
2	chr2:152329723..152332173-chr2:152332317..152334542,2	K562	blood:
3	chr2:152333499..152335226-chr2:152337769..152339551,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TNFAIP6-5	chr2:152332640-152333850	NONHSAT074957

Variant related genes	Relation type
ENSG00000080345	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10167358	0.81[CEU][hapmap];0.87[CHB][hapmap]
rs10173699	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10175134	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10497081	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10497082	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1061305	0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs11675385	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11892439	0.88[CHB][hapmap]
rs12618981	0.88[CEU][hapmap];0.88[CHB][hapmap];0.83[JPT][hapmap];0.80[EUR][1000 genomes]
rs12994320	0.83[AFR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13393021	0.87[CEU][hapmap]
rs13403719	0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13425170	1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs13555	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17193268	0.80[EUR][1000 genomes]
rs17270233	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17806204	0.88[CEU][hapmap];0.80[EUR][1000 genomes]
rs2045025	0.93[AFR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2288193	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2288196	0.86[YRI][hapmap]
rs2342911	0.86[AFR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2432942	0.95[ASN][1000 genomes]
rs2432943	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2432945	0.86[AFR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2432946	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs2432953	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2432954	0.98[AFR][1000 genomes];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2432956	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs2432957	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs2444256	0.83[CEU][hapmap];0.86[YRI][hapmap];0.84[EUR][1000 genomes]
rs2444264	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2444267	0.90[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs4335940	0.86[AFR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4461258	0.86[CEU][hapmap];0.81[CHB][hapmap];0.88[JPT][hapmap]
rs4467261	0.80[AFR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4500942	0.80[CEU][hapmap];0.87[EUR][1000 genomes]
rs4592848	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4664438	0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4664490	0.80[CHB][hapmap]
rs4664491	0.88[CHB][hapmap]
rs5024580	0.84[EUR][1000 genomes]
rs6718372	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs6718653	0.96[ASN][1000 genomes]
rs6721666	0.87[YRI][hapmap]
rs6724796	0.87[CEU][hapmap]
rs6730454	0.87[YRI][hapmap]
rs6731486	0.87[CEU][hapmap]
rs6735771	0.86[AFR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72860233	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7587301	0.89[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs7608474	0.95[ASN][1000 genomes]
rs9287979	0.82[YRI][hapmap]

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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1047957	RIF1	cis	Skin Sun Exposed Lower leg	GTEx
rs1047957	RIF1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:152267600-152379400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr2:152267800-152340400	Weak transcription	Stomach Mucosa	stomach
3	chr2:152268000-152342800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr2:152268600-152334400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr2:152268600-152342600	Strong transcription	HUES6 Cell Line	embryonic stem cell
6	chr2:152283800-152334000	Strong transcription	Primary T cells fromperipheralblood	blood
7	chr2:152295800-152348400	Weak transcription	Right Ventricle	heart
8	chr2:152301800-152343800	Weak transcription	Gastric	stomach
9	chr2:152304800-152354000	Weak transcription	Spleen	Spleen
10	chr2:152314000-152344000	Weak transcription	Esophagus	oesophagus
11	chr2:152314000-152349400	Weak transcription	Pancreas	Pancrea
12	chr2:152319000-152338200	Weak transcription	Lung	lung
13	chr2:152320400-152336400	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr2:152320400-152339200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
15	chr2:152320400-152343800	Strong transcription	HUES48 Cell Line	embryonic stem cell
16	chr2:152320800-152343600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
17	chr2:152320800-152358600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr2:152321400-152340200	Weak transcription	Psoas Muscle	Psoas
19	chr2:152324000-152334400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr2:152324000-152348800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr2:152324200-152382400	Weak transcription	Aorta	Aorta
22	chr2:152325600-152348800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr2:152326200-152344200	Weak transcription	Brain Cingulate Gyrus	brain
24	chr2:152326200-152347400	Weak transcription	Rectal Smooth Muscle	rectum
25	chr2:152326400-152367400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr2:152326600-152348000	Weak transcription	Brain Substantia Nigra	brain
27	chr2:152327000-152338200	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr2:152327000-152338200	Weak transcription	HSMMtube	muscle
29	chr2:152327200-152339000	Weak transcription	Ovary	ovary
30	chr2:152327200-152340600	Weak transcription	Stomach Smooth Muscle	stomach
31	chr2:152327200-152342600	Weak transcription	Small Intestine	intestine
32	chr2:152327200-152343800	Weak transcription	Thymus	Thymus
33	chr2:152327200-152347400	Weak transcription	Brain Angular Gyrus	brain
34	chr2:152327400-152337200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr2:152327400-152338400	Weak transcription	Colonic Mucosa	Colon
36	chr2:152327400-152340000	Weak transcription	Fetal Brain Female	brain
37	chr2:152327400-152342800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr2:152327400-152343400	Weak transcription	Fetal Brain Male	brain
39	chr2:152327400-152344800	Weak transcription	Brain Anterior Caudate	brain
40	chr2:152327600-152337800	Weak transcription	Fetal Heart	heart
41	chr2:152327600-152339000	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr2:152327600-152339000	Weak transcription	NHLF	lung
43	chr2:152327800-152335000	Weak transcription	Duodenum Mucosa	Duodenum
44	chr2:152327800-152336000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr2:152327800-152340200	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr2:152327800-152340200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr2:152327800-152340400	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr2:152327800-152342600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr2:152327800-152346800	Weak transcription	Colon Smooth Muscle	Colon
50	chr2:152327800-152347800	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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