Variant report

Variant	rs13400920
Chromosome Location	chr2:73337088-73337089
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA2	chr2:73336338-73337205	SH-SY5Y	brain:	n/a	n/a
2	RCOR1	chr2:73337004-73337207	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr2:73332373-73337395	K562	blood:	n/a	n/a
4	RCOR1	chr2:73337024-73337245	K562	blood:	n/a	n/a
5	RCOR1	chr2:73336945-73337272	K562	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:73332810..73335767-chr2:73335850..73338360,4	K562	blood:
2	chr2:73336661..73339816-chr2:73350346..73353019,4	K562	blood:
3	chr2:73336788..73338618-chr2:73338924..73341892,2	K562	blood:
4	chr2:73324923..73326792-chr2:73335273..73337149,2	K562	blood:
5	chr2:73330344..73333243-chr2:73334640..73337340,3	MCF-7	breast:
6	chr2:73295259..73298066-chr2:73336566..73338482,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000272702	TF binding region
ENSG00000272702	Chromatin interaction
ENSG00000135631	Chromatin interaction
ENSG00000144040	Chromatin interaction

Extended variants
information (count: 104 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:102)

rs_ID	r²[population]
rs10166220	0.91[JPT][hapmap]
rs10167566	0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs10174548	0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10176939	0.86[JPT][hapmap];0.85[YRI][hapmap]
rs10177159	0.81[JPT][hapmap]
rs10180720	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]
rs10180995	0.94[ASW][hapmap];0.94[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10189744	0.91[JPT][hapmap]
rs10190861	0.87[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10192077	0.94[ASW][hapmap];0.81[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];0.90[MEX][hapmap];0.97[MKK][hapmap];0.90[TSI][hapmap];0.88[YRI][hapmap];0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10197305	0.86[JPT][hapmap];0.86[MEX][hapmap];0.90[TSI][hapmap]
rs10203608	0.90[ASN][1000 genomes]
rs1046186	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10865396	0.92[ASN][1000 genomes]
rs11126389	0.92[ASN][1000 genomes]
rs11686557	0.82[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs11885522	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12104691	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12233055	0.81[JPT][hapmap];0.90[MEX][hapmap];0.90[TSI][hapmap]
rs12614059	0.94[ASN][1000 genomes]
rs13018842	0.92[ASN][1000 genomes]
rs13019020	0.81[ASN][1000 genomes]
rs13385994	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13388404	0.91[JPT][hapmap]
rs13390072	0.83[EUR][1000 genomes]
rs13391532	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13393567	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13400948	0.94[ASW][hapmap];0.82[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];0.90[MEX][hapmap];0.85[MKK][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs13403757	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs13403781	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs13407719	0.88[ASN][1000 genomes]
rs13416407	0.87[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13427947	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1370383	0.90[MEX][hapmap];0.90[TSI][hapmap]
rs1430349	0.94[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1430350	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1430351	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17008571	0.86[JPT][hapmap];0.81[YRI][hapmap]
rs17008611	0.81[JPT][hapmap];0.81[MEX][hapmap];0.86[TSI][hapmap]
rs17008631	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1864488	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.99[ASN][1000 genomes]
rs1992133	0.94[ASW][hapmap];0.94[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.93[LWK][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2421098	0.83[CHD][hapmap];0.91[JPT][hapmap]
rs35131031	0.89[ASN][1000 genomes]
rs3813222	0.94[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3813223	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3901273	0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4144837	0.82[CEU][hapmap];0.91[JPT][hapmap];0.81[YRI][hapmap];0.81[EUR][1000 genomes]
rs4514897	0.81[CHD][hapmap];0.91[JPT][hapmap]
rs4591365	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55894650	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57536428	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57701326	0.96[ASN][1000 genomes]
rs57726945	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57937746	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6546796	0.81[JPT][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap]
rs6546797	0.83[ASW][hapmap];0.81[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.86[TSI][hapmap];0.92[YRI][hapmap]
rs6546800	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6546801	0.99[ASN][1000 genomes]
rs6709938	0.86[JPT][hapmap]
rs6710739	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]
rs6710755	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.81[LWK][hapmap];0.86[MEX][hapmap];0.82[MKK][hapmap];0.81[YRI][hapmap];0.82[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs6711891	0.86[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.82[YRI][hapmap]
rs6712925	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6713655	0.83[EUR][1000 genomes]
rs6719333	0.91[JPT][hapmap];0.89[YRI][hapmap]
rs6720817	0.89[ASN][1000 genomes]
rs6726940	0.81[JPT][hapmap]
rs6727269	0.83[EUR][1000 genomes]
rs6727919	0.94[ASW][hapmap];0.88[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];0.96[TSI][hapmap];0.82[YRI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6729266	0.82[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.90[ASN][1000 genomes]
rs6732369	0.91[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap]
rs6736153	0.83[ASW][hapmap];0.82[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6749237	0.82[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6750069	0.86[JPT][hapmap];0.89[YRI][hapmap]
rs6754779	0.83[EUR][1000 genomes]
rs6754858	0.83[EUR][1000 genomes]
rs6757131	0.86[JPT][hapmap]
rs6759733	0.80[JPT][hapmap];0.86[MEX][hapmap]
rs727470	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs727471	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs732179	0.81[JPT][hapmap]
rs732180	0.80[JPT][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap]
rs7557173	0.88[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.94[ASN][1000 genomes]
rs7559074	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7559340	0.94[CEU][hapmap];0.95[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7566904	0.83[ASW][hapmap];0.82[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.84[LWK][hapmap];0.95[MEX][hapmap];0.90[MKK][hapmap];0.90[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7567413	0.81[ASN][1000 genomes]
rs7570459	0.81[ASN][1000 genomes]
rs7570876	0.91[JPT][hapmap];0.85[YRI][hapmap]
rs7579770	0.86[JPT][hapmap]
rs7580216	0.81[JPT][hapmap];0.90[MEX][hapmap];0.90[TSI][hapmap]
rs7593322	0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7596830	0.81[ASN][1000 genomes]
rs7597032	0.86[JPT][hapmap]
rs7599657	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7602651	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs891432	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs891433	0.89[ASW][hapmap];0.88[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs893258	0.86[JPT][hapmap]
rs893259	0.86[JPT][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap]
rs9309471	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[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	nsv1006801	chr2:73305056-73431711	Weak transcription Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13400920	SFXN5	cis	cerebellum	SCAN

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:73315600-73338000	Weak transcription	Primary T helper cells fromperipheralblood	blood
2	chr2:73316200-73338400	Weak transcription	Brain Germinal Matrix	brain
3	chr2:73327000-73338800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:73329400-73338200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr2:73329600-73337600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr2:73329800-73337800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr2:73330400-73337400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr2:73330400-73337400	Weak transcription	Fetal Lung	lung
9	chr2:73330600-73337800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr2:73330800-73337800	Enhancers	Placenta	Placenta
11	chr2:73330800-73338200	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr2:73331200-73337600	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr2:73331200-73337600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr2:73331400-73337200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr2:73332400-73337600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr2:73332800-73337200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr2:73332800-73337400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr2:73333800-73337800	Enhancers	HepG2	liver
19	chr2:73334600-73338000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr2:73334800-73337200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr2:73334800-73337400	Enhancers	Brain Angular Gyrus	brain
22	chr2:73334800-73337800	Weak transcription	Fetal Brain Female	brain
23	chr2:73335000-73337200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr2:73335000-73337200	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr2:73335000-73337200	Weak transcription	HMEC	breast
26	chr2:73335000-73338200	Weak transcription	Stomach Mucosa	stomach
27	chr2:73335200-73337400	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr2:73335200-73337400	Weak transcription	Adipose Nuclei	Adipose
29	chr2:73335200-73337400	Weak transcription	Colonic Mucosa	Colon
30	chr2:73335200-73337400	Weak transcription	Esophagus	oesophagus
31	chr2:73335200-73337400	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr2:73335200-73337800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr2:73335200-73337800	Weak transcription	Aorta	Aorta
34	chr2:73335200-73337800	Weak transcription	Duodenum Mucosa	Duodenum
35	chr2:73335200-73337800	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr2:73335400-73337200	Weak transcription	Fetal Intestine Small	intestine
37	chr2:73335400-73337200	Weak transcription	Osteobl	bone
38	chr2:73335400-73338000	Weak transcription	Brain Hippocampus Middle	brain
39	chr2:73335400-73338200	Weak transcription	Brain Substantia Nigra	brain
40	chr2:73335600-73337200	Weak transcription	Ovary	ovary
41	chr2:73335600-73337400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr2:73335600-73337600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr2:73335600-73337800	Weak transcription	Psoas Muscle	Psoas
44	chr2:73335600-73338200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr2:73335800-73337200	Weak transcription	Brain Cingulate Gyrus	brain
46	chr2:73335800-73337200	Weak transcription	Pancreas	Pancrea
47	chr2:73335800-73337200	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr2:73335800-73337200	Weak transcription	HSMM	muscle
49	chr2:73335800-73337200	Weak transcription	NH-A	brain
50	chr2:73335800-73337800	Weak transcription	Fetal Stomach	stomach

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