Variant report

Variant	rs6710739
Chromosome Location	chr2:73278990-73278991
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:73270996..73273259-chr2:73277285..73279841,3	K562	blood:

Variant related genes	Relation type
ENSG00000144040	Chromatin interaction

Extended variants
information (count: 117 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:115)

rs_ID	r²[population]
rs10166058	0.83[EUR][1000 genomes]
rs10166220	0.93[CEU][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10167566	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs10174548	0.86[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.92[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];0.80[EUR][1000 genomes]
rs10178854	0.83[EUR][1000 genomes]
rs10178944	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10180720	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]
rs10180995	0.94[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10189744	0.93[CEU][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes]
rs10190861	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10191665	0.83[EUR][1000 genomes]
rs10192077	0.94[ASW][hapmap];0.93[CEU][hapmap];0.80[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];0.90[MEX][hapmap];0.84[MKK][hapmap];0.96[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10197305	0.87[CEU][hapmap];0.85[GIH][hapmap];0.90[JPT][hapmap];0.96[TSI][hapmap];0.82[EUR][1000 genomes]
rs10203608	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10209859	0.87[CEU][hapmap]
rs1036512	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1046186	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10865396	0.80[ASN][1000 genomes]
rs11126389	0.80[ASN][1000 genomes]
rs11686557	0.86[ASN][1000 genomes]
rs11885522	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12104691	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12233055	0.93[CEU][hapmap];0.86[JPT][hapmap];0.90[MEX][hapmap];0.96[TSI][hapmap];0.83[EUR][1000 genomes]
rs12614059	0.82[ASN][1000 genomes]
rs13018842	0.80[ASN][1000 genomes]
rs13385994	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13388404	0.87[CEU][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes]
rs13390072	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13391532	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13393567	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13400920	0.88[ASW][hapmap];0.82[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.82[MKK][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13400948	0.82[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap];0.96[ASN][1000 genomes]
rs13403757	0.86[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs13403781	0.86[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs13407719	0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs13416407	0.81[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13427947	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1370383	0.86[CEU][hapmap];0.87[GIH][hapmap];0.81[JPT][hapmap];0.81[MEX][hapmap];0.96[TSI][hapmap];0.81[EUR][1000 genomes]
rs1430349	0.87[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1430350	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1430351	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[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];0.80[MEX][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs17008631	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1864488	0.95[CHB][hapmap];0.91[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.87[ASN][1000 genomes]
rs1992133	0.94[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.82[MKK][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2421098	0.95[JPT][hapmap]
rs3813222	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3813223	0.88[ASN][1000 genomes]
rs3901273	0.86[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4144837	1.00[CEU][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4514897	0.80[CHD][hapmap];0.95[JPT][hapmap]
rs4527230	0.81[EUR][1000 genomes]
rs4591365	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55894650	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55974516	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs57536428	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57701326	0.91[ASN][1000 genomes]
rs57726945	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57937746	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58993488	0.81[EUR][1000 genomes]
rs61161134	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61650913	0.83[EUR][1000 genomes]
rs62147721	0.81[EUR][1000 genomes]
rs62147724	0.82[EUR][1000 genomes]
rs62147732	0.83[EUR][1000 genomes]
rs6546794	0.82[EUR][1000 genomes]
rs6546796	0.87[CEU][hapmap];0.87[GIH][hapmap];0.85[JPT][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs6546797	0.83[ASW][hapmap];0.87[CEU][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6546800	0.87[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6546801	0.87[ASN][1000 genomes]
rs6709938	0.87[CEU][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes]
rs6710755	0.95[CHB][hapmap];0.91[CHD][hapmap];0.83[GIH][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs6711891	0.87[CEU][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap];0.96[TSI][hapmap]
rs6712925	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6713655	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6719333	0.93[CEU][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6720817	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6726940	0.87[CEU][hapmap];0.86[JPT][hapmap];0.81[EUR][1000 genomes]
rs6727269	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6727919	0.82[ASW][hapmap];0.93[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6729266	0.86[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap];0.95[ASN][1000 genomes]
rs6732369	0.87[CEU][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.96[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6736153	0.86[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.92[ASN][1000 genomes]
rs6749237	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6750069	0.93[CEU][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes]
rs6754779	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6754858	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6757131	0.93[CEU][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes]
rs6759243	0.83[EUR][1000 genomes]
rs6759733	0.93[CEU][hapmap];0.81[GIH][hapmap];0.85[JPT][hapmap];0.80[EUR][1000 genomes]
rs727470	0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs727471	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[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];0.90[MEX][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes]
rs7557173	0.80[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7559074	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7559340	0.87[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7566904	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.90[MKK][hapmap];0.96[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[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];0.90[MEX][hapmap];0.96[TSI][hapmap];0.83[EUR][1000 genomes]
rs7593322	0.90[ASN][1000 genomes]
rs7597032	0.87[CEU][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes]
rs7599657	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7602651	0.88[ASW][hapmap];0.87[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.82[MKK][hapmap];0.96[TSI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs891432	0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs891433	0.93[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs893258	0.90[JPT][hapmap]
rs893259	0.87[CEU][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs9309467	0.82[EUR][1000 genomes]
rs9309471	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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
2	esv20443	chr2:73270284-73280427	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6710739	SFXN5	cis	cerebellum	SCAN

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:73214200-73286400	Weak transcription	Psoas Muscle	Psoas
2	chr2:73246600-73283800	Weak transcription	Hela-S3	cervix
3	chr2:73247400-73283800	Weak transcription	Dnd41	blood
4	chr2:73249400-73284200	Weak transcription	Aorta	Aorta
5	chr2:73249400-73290000	Weak transcription	HUVEC	blood vessel
6	chr2:73249600-73290000	Weak transcription	NHLF	lung
7	chr2:73250200-73284200	Weak transcription	Ovary	ovary
8	chr2:73253200-73280800	Weak transcription	Fetal Lung	lung
9	chr2:73256800-73279400	Weak transcription	Osteobl	bone
10	chr2:73256800-73280200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr2:73256800-73290000	Weak transcription	HSMM	muscle
12	chr2:73259200-73291200	Weak transcription	Small Intestine	intestine
13	chr2:73260200-73284200	Weak transcription	Duodenum Mucosa	Duodenum
14	chr2:73260600-73284400	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr2:73260800-73279200	Weak transcription	Fetal Intestine Large	intestine
16	chr2:73260800-73283800	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr2:73261400-73282000	Weak transcription	Adipose Nuclei	Adipose
18	chr2:73261400-73284200	Weak transcription	Gastric	stomach
19	chr2:73262400-73280400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr2:73262800-73290600	Weak transcription	NHEK	skin
21	chr2:73264000-73280800	Weak transcription	Fetal Muscle Trunk	muscle
22	chr2:73264200-73290600	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr2:73264400-73280000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr2:73264600-73284400	Weak transcription	Esophagus	oesophagus
25	chr2:73265600-73283800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr2:73267800-73289400	Weak transcription	K562	blood
27	chr2:73268000-73280400	Weak transcription	Brain Hippocampus Middle	brain
28	chr2:73268000-73280800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr2:73268000-73281800	Weak transcription	A549	lung
30	chr2:73268000-73284000	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr2:73268200-73280000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr2:73268200-73280400	Weak transcription	Brain Cingulate Gyrus	brain
33	chr2:73268200-73280600	Weak transcription	Colon Smooth Muscle	Colon
34	chr2:73268200-73280800	Weak transcription	Left Ventricle	heart
35	chr2:73268200-73284200	Weak transcription	Lung	lung
36	chr2:73268400-73279000	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr2:73268400-73282200	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr2:73268400-73283800	Weak transcription	Fetal Muscle Leg	muscle
39	chr2:73268600-73280200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr2:73268600-73281600	Weak transcription	Stomach Smooth Muscle	stomach
41	chr2:73268600-73289400	Weak transcription	Right Ventricle	heart
42	chr2:73269000-73283000	Weak transcription	Primary B cells from cord blood	blood
43	chr2:73270200-73279000	Weak transcription	Primary monocytes fromperipheralblood	blood
44	chr2:73270400-73280400	Weak transcription	Brain Angular Gyrus	brain
45	chr2:73270600-73281600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr2:73271200-73280800	Weak transcription	Right Atrium	heart
47	chr2:73272000-73279200	Weak transcription	Brain Anterior Caudate	brain
48	chr2:73272000-73282200	Weak transcription	Fetal Intestine Small	intestine
49	chr2:73272000-73283600	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr2:73272200-73283600	Weak transcription	Primary T cells fromperipheralblood	blood

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