Variant report

Variant	rs10180720
Chromosome Location	chr2:73285752-73285753
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:73284849..73288387-chr2:73297041..73300553,5	K562	blood:

Variant related genes	Relation type
ENSG00000144040	Chromatin interaction

Extended variants
information (count: 117 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:116)

rs_ID	r²[population]
rs10166058	0.83[EUR][1000 genomes]
rs10166220	0.93[CEU][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10167566	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10174548	0.86[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10176939	0.93[CEU][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes]
rs10177159	0.87[CEU][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes]
rs10178854	0.84[EUR][1000 genomes]
rs10178944	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10180995	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.90[TSI][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10189744	0.93[CEU][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes]
rs10190861	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10191665	0.84[EUR][1000 genomes]
rs10192077	0.93[CEU][hapmap];0.83[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10197305	0.87[CEU][hapmap];0.85[GIH][hapmap];0.90[JPT][hapmap];0.81[MEX][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes]
rs10203608	0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10209859	0.87[CEU][hapmap];0.81[EUR][1000 genomes]
rs1036512	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1046186	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10865396	0.82[ASN][1000 genomes]
rs11126389	0.82[ASN][1000 genomes]
rs11686557	0.87[ASN][1000 genomes]
rs11885522	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12104691	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12233055	0.93[CEU][hapmap];0.86[JPT][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs12614059	0.84[ASN][1000 genomes]
rs13018842	0.82[ASN][1000 genomes]
rs13385994	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13388404	0.87[CEU][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes]
rs13390072	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13391532	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13393567	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13400920	0.82[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13400948	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.85[MEX][hapmap];0.98[ASN][1000 genomes]
rs13403757	0.86[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs13403781	0.86[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs13407719	0.90[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs13416407	0.81[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13427947	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1370383	0.86[CEU][hapmap];0.87[GIH][hapmap];0.81[JPT][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs1430349	0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1430350	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1430351	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17008571	0.87[CEU][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes]
rs17008611	0.87[CEU][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];0.96[TSI][hapmap];0.84[EUR][1000 genomes]
rs17008631	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1864488	0.95[CHB][hapmap];0.98[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap];0.88[ASN][1000 genomes]
rs1992133	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.90[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2421098	0.85[CHD][hapmap];0.95[JPT][hapmap]
rs3813222	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3813223	0.89[ASN][1000 genomes]
rs3901273	0.86[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4144837	1.00[CEU][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4514897	0.83[CHD][hapmap];0.95[JPT][hapmap]
rs4527230	0.81[EUR][1000 genomes]
rs4591365	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55894650	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55974516	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs57536428	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57701326	0.92[ASN][1000 genomes]
rs57726945	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57937746	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58993488	0.81[EUR][1000 genomes]
rs61161134	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61650913	0.84[EUR][1000 genomes]
rs62147721	0.81[EUR][1000 genomes]
rs62147724	0.82[EUR][1000 genomes]
rs62147732	0.84[EUR][1000 genomes]
rs6546794	0.82[EUR][1000 genomes]
rs6546796	0.87[CEU][hapmap];0.87[GIH][hapmap];0.85[JPT][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.84[EUR][1000 genomes]
rs6546797	0.88[ASW][hapmap];0.87[CEU][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6546800	0.87[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6546801	0.88[ASN][1000 genomes]
rs6709938	0.87[CEU][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes]
rs6710739	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.90[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6710755	0.95[CHB][hapmap];0.98[CHD][hapmap];0.83[GIH][hapmap];0.91[JPT][hapmap];0.81[MEX][hapmap];0.88[ASN][1000 genomes]
rs6711891	0.87[CEU][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap]
rs6712925	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6713655	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6717553	0.81[EUR][1000 genomes]
rs6719333	0.93[CEU][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6720817	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6726940	0.87[CEU][hapmap];0.86[JPT][hapmap];0.81[EUR][1000 genomes]
rs6727269	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6727919	0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6729266	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.96[ASN][1000 genomes]
rs6732369	0.87[CEU][hapmap];0.80[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6736153	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.94[ASN][1000 genomes]
rs6749237	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6750069	0.93[CEU][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes]
rs6754779	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6754858	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6757131	0.93[CEU][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes]
rs6759243	0.85[EUR][1000 genomes]
rs6759733	0.93[CEU][hapmap];0.81[GIH][hapmap];0.85[JPT][hapmap];0.81[MEX][hapmap];0.82[EUR][1000 genomes]
rs727470	0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs727471	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs732178	0.93[CEU][hapmap];0.81[JPT][hapmap];0.83[EUR][1000 genomes]
rs732179	0.93[CEU][hapmap];0.86[JPT][hapmap];0.83[EUR][1000 genomes]
rs732180	0.93[CEU][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.83[EUR][1000 genomes]
rs7557173	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7559074	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7559340	0.87[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7566904	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7570876	0.87[CEU][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7579770	0.87[CEU][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes]
rs7580216	0.93[CEU][hapmap];0.84[GIH][hapmap];0.86[JPT][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs7593322	0.92[ASN][1000 genomes]
rs7597032	0.87[CEU][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes]
rs7599657	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7602651	0.87[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs891432	0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs891433	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs893258	0.90[JPT][hapmap]
rs893259	0.87[CEU][hapmap];0.90[JPT][hapmap];0.86[MEX][hapmap];0.96[TSI][hapmap];0.81[EUR][1000 genomes]
rs9309467	0.82[EUR][1000 genomes]
rs9309471	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002295	chr2:73216155-73350391	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10180720	SFXN5	cis	cerebellum	SCAN
rs10180720	RAB11FIP5	cis	multi-tissue	Pritchard

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:73214200-73286400	Weak transcription	Psoas Muscle	Psoas
2	chr2:73249400-73290000	Weak transcription	HUVEC	blood vessel
3	chr2:73249600-73290000	Weak transcription	NHLF	lung
4	chr2:73256800-73290000	Weak transcription	HSMM	muscle
5	chr2:73259200-73291200	Weak transcription	Small Intestine	intestine
6	chr2:73262800-73290600	Weak transcription	NHEK	skin
7	chr2:73264200-73290600	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr2:73267800-73289400	Weak transcription	K562	blood
9	chr2:73268600-73289400	Weak transcription	Right Ventricle	heart
10	chr2:73272600-73291200	Weak transcription	Fetal Heart	heart
11	chr2:73275800-73297000	Weak transcription	Pancreas	Pancrea
12	chr2:73277800-73285800	Weak transcription	Fetal Brain Male	brain
13	chr2:73277800-73290400	Weak transcription	HMEC	breast
14	chr2:73277800-73290800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr2:73277800-73291200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr2:73281200-73289800	Weak transcription	NHDF-Ad	bronchial
17	chr2:73283200-73285800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
18	chr2:73283400-73285800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr2:73283400-73286000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr2:73283400-73286400	ZNF genes & repeats	Fetal Intestine Small	intestine
21	chr2:73283600-73285800	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr2:73283600-73286000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr2:73283600-73286400	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
24	chr2:73283800-73285800	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
25	chr2:73283800-73285800	ZNF genes & repeats	Dnd41	blood
26	chr2:73283800-73286200	Strong transcription	Primary T cells from cord blood	blood
27	chr2:73283800-73286200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr2:73284000-73285800	Strong transcription	Left Ventricle	heart
29	chr2:73284000-73286400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr2:73284200-73285800	ZNF genes & repeats	Aorta	Aorta
31	chr2:73284200-73285800	Strong transcription	Skeletal Muscle Female	skeletal muscle
32	chr2:73284200-73286200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr2:73284200-73287000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr2:73284200-73290000	Weak transcription	Hela-S3	cervix
35	chr2:73284400-73286000	Strong transcription	Esophagus	oesophagus
36	chr2:73284600-73285800	Strong transcription	Fetal Muscle Leg	muscle
37	chr2:73284600-73285800	Weak transcription	GM12878-XiMat	blood
38	chr2:73284600-73286200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr2:73284600-73286200	Strong transcription	Primary neutrophils fromperipheralblood	blood
40	chr2:73284600-73286800	Strong transcription	HepG2	liver
41	chr2:73284600-73290000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr2:73284600-73290600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr2:73284600-73296600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr2:73284800-73285800	Weak transcription	Brain Hippocampus Middle	brain
45	chr2:73284800-73286000	Strong transcription	Fetal Stomach	stomach
46	chr2:73284800-73290200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr2:73284800-73296400	Weak transcription	Fetal Kidney	kidney
48	chr2:73285000-73286000	Strong transcription	Liver	Liver
49	chr2:73285000-73286000	Weak transcription	Brain Angular Gyrus	brain
50	chr2:73285000-73286000	Weak transcription	Brain Cingulate Gyrus	brain

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