Variant report

Variant	rs1061305
Chromosome Location	chr2:152346979-152346980
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:152346891-152347047	MCF-7	breast:	n/a	n/a
2	POLR2A	chr2:152346876-152347078	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:152344851..152347246-chr2:152350528..152353460,3	K562	blood:
2	chr2:152345538..152348326-chr2:152350633..152352626,2	MCF-7	breast:

Variant related genes	Relation type
RIF1	TF binding region
ENSG00000080345	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10167358	0.88[CHD][hapmap]
rs10173699	0.88[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs10175134	0.87[ASN][1000 genomes]
rs1047957	0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs10497081	0.93[ASN][1000 genomes]
rs10497082	0.88[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12618981	0.82[JPT][hapmap]
rs12994320	0.83[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs13403719	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13425170	0.88[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs13555	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs17270233	0.86[ASN][1000 genomes]
rs2045025	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2288193	0.87[CHB][hapmap];0.94[JPT][hapmap];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2288196	0.86[YRI][hapmap]
rs2342911	0.80[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs2432942	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2432943	0.94[ASN][1000 genomes]
rs2432945	0.80[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs2432946	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2432953	0.95[ASN][1000 genomes]
rs2432954	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2432956	0.96[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2432957	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2444256	0.91[LWK][hapmap];0.81[MKK][hapmap];0.86[YRI][hapmap]
rs2444264	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2444267	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3771901	0.86[CHD][hapmap]
rs4335940	0.80[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs4461258	0.89[CHD][hapmap];0.88[JPT][hapmap]
rs4467261	0.87[ASN][1000 genomes]
rs4592848	0.88[CHB][hapmap];0.94[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4664438	0.97[ASN][1000 genomes]
rs6718372	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6718653	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6721666	0.86[YRI][hapmap]
rs6730454	0.86[YRI][hapmap]
rs6735771	0.80[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs72860233	0.92[ASN][1000 genomes]
rs7587301	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7608474	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9287979	0.80[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
rs1061305	RIF1	cis	parietal	SCAN
rs1061305	RIF1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:88 , 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	chr2:152295800-152348400	Weak transcription	Right Ventricle	heart
3	chr2:152304800-152354000	Weak transcription	Spleen	Spleen
4	chr2:152314000-152349400	Weak transcription	Pancreas	Pancrea
5	chr2:152320800-152358600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr2:152324000-152348800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr2:152324200-152382400	Weak transcription	Aorta	Aorta
8	chr2:152325600-152348800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr2:152326200-152347400	Weak transcription	Rectal Smooth Muscle	rectum
10	chr2:152326400-152367400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr2:152326600-152348000	Weak transcription	Brain Substantia Nigra	brain
12	chr2:152327200-152347400	Weak transcription	Brain Angular Gyrus	brain
13	chr2:152327800-152347800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr2:152328400-152347000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr2:152332000-152350400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr2:152332400-152350800	Weak transcription	NHDF-Ad	bronchial
17	chr2:152334000-152349400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr2:152335200-152349400	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr2:152336800-152355000	Strong transcription	Fetal Muscle Leg	muscle
20	chr2:152337400-152348800	Weak transcription	Hela-S3	cervix
21	chr2:152338200-152356600	Strong transcription	HSMMtube	muscle
22	chr2:152338200-152370000	Strong transcription	Skeletal Muscle Male	skeletal muscle
23	chr2:152338400-152347200	Weak transcription	HMEC	breast
24	chr2:152338400-152349000	Weak transcription	HUVEC	blood vessel
25	chr2:152338600-152348800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr2:152338600-152358200	Weak transcription	Primary T helper cells PMA-I stimulated	--
27	chr2:152339400-152348200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr2:152339400-152348600	Weak transcription	Ovary	ovary
29	chr2:152339400-152350800	Weak transcription	A549	lung
30	chr2:152339600-152354400	Weak transcription	Primary hematopoietic stem cells	blood
31	chr2:152339800-152350400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr2:152340400-152348400	Weak transcription	NHLF	lung
33	chr2:152340400-152349800	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr2:152340400-152350000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr2:152340400-152371000	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr2:152340600-152364600	Weak transcription	HepG2	liver
37	chr2:152341200-152366200	Weak transcription	Primary T cells fromperipheralblood	blood
38	chr2:152341400-152348400	Weak transcription	Brain Germinal Matrix	brain
39	chr2:152341400-152350200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr2:152341600-152347000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
41	chr2:152341600-152347400	Weak transcription	Primary neutrophils fromperipheralblood	blood
42	chr2:152341600-152348600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr2:152341600-152353400	Weak transcription	NHEK	skin
44	chr2:152341600-152390600	Weak transcription	Left Ventricle	heart
45	chr2:152341800-152347600	Weak transcription	Fetal Stomach	stomach
46	chr2:152341800-152350000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr2:152341800-152350400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr2:152341800-152350800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr2:152341800-152364400	Weak transcription	Fetal Intestine Small	intestine
50	chr2:152342000-152347000	Weak transcription	Stomach Smooth Muscle	stomach

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