Variant report

Variant	rs13400948
Chromosome Location	chr2:73289887-73289888
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	BHLHE40	chr2:73289782-73289915	K562	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr2:73267482..73270454-chr2:73289575..73291356,2	K562	blood:
2	chr2:73285227..73287665-chr2:73288281..73291317,3	K562	blood:
3	chr2:73287986..73293083-chr2:73295177..73299013,8	MCF-7	breast:
4	chr2:73289263..73291570-chr2:73296158..73299685,4	MCF-7	breast:
5	chr2:73282143..73284248-chr2:73287345..73289978,3	K562	blood:

No data

Variant related genes	Relation type
SFXN5	TF binding region
ENSG00000144040	Chromatin interaction

Extended variants
information (count: 94 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs10166220	0.80[CEU][hapmap];0.86[JPT][hapmap]
rs10167566	0.93[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10174548	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10176939	0.80[CEU][hapmap];0.81[JPT][hapmap];0.82[YRI][hapmap]
rs10180720	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]
rs10180995	0.88[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.90[JPT][hapmap];0.85[MEX][hapmap];0.95[ASN][1000 genomes]
rs10189744	0.80[CEU][hapmap];0.86[JPT][hapmap]
rs10190861	0.93[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs10192077	0.88[ASW][hapmap];0.80[CEU][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.83[LWK][hapmap];0.90[MEX][hapmap];0.88[MKK][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs10197305	0.82[GIH][hapmap];0.81[JPT][hapmap]
rs10203608	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1046186	0.98[ASN][1000 genomes]
rs10865396	0.81[ASN][1000 genomes]
rs11126389	0.81[ASN][1000 genomes]
rs11686557	0.88[ASN][1000 genomes]
rs11885522	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12104691	0.95[ASN][1000 genomes]
rs12233055	0.80[CEU][hapmap];0.90[MEX][hapmap]
rs12614059	0.84[ASN][1000 genomes]
rs13018842	0.81[ASN][1000 genomes]
rs13385994	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs13388404	0.86[JPT][hapmap]
rs13391532	0.92[ASN][1000 genomes]
rs13393567	0.99[ASN][1000 genomes]
rs13400920	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	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13403781	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13407719	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13416407	0.81[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.82[YRI][hapmap];0.95[ASN][1000 genomes]
rs13427947	0.80[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1370383	0.84[GIH][hapmap];0.81[MEX][hapmap]
rs1430349	0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.88[ASN][1000 genomes]
rs1430350	0.92[ASN][1000 genomes]
rs1430351	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs17008571	0.81[JPT][hapmap]
rs17008611	0.85[GIH][hapmap];0.80[MEX][hapmap]
rs17008631	0.86[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1864488	0.95[CHB][hapmap];0.98[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.89[ASN][1000 genomes]
rs1992133	0.88[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.85[JPT][hapmap];0.85[MKK][hapmap];0.81[YRI][hapmap];0.81[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs2421098	0.85[CHD][hapmap];0.86[JPT][hapmap]
rs3813222	0.87[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs3813223	0.90[ASN][1000 genomes]
rs3901273	0.86[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs4144837	0.86[CEU][hapmap];0.86[JPT][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes]
rs4514897	0.83[CHD][hapmap];0.86[JPT][hapmap]
rs4591365	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs55894650	0.92[ASN][1000 genomes]
rs57536428	0.98[ASN][1000 genomes]
rs57701326	0.92[ASN][1000 genomes]
rs57726945	0.88[ASN][1000 genomes]
rs57937746	0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6546796	0.85[GIH][hapmap];0.86[MEX][hapmap]
rs6546797	0.85[GIH][hapmap];0.90[MEX][hapmap];0.82[YRI][hapmap]
rs6546800	0.87[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.94[ASN][1000 genomes]
rs6546801	0.89[ASN][1000 genomes]
rs6709938	0.81[JPT][hapmap]
rs6710739	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]
rs6710755	0.95[CHB][hapmap];0.98[CHD][hapmap];0.81[GIH][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs6711891	0.81[JPT][hapmap];0.90[MEX][hapmap];0.83[YRI][hapmap]
rs6712925	0.94[ASN][1000 genomes]
rs6719333	0.80[CEU][hapmap];0.86[JPT][hapmap];0.86[YRI][hapmap]
rs6720817	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6727269	0.81[AMR][1000 genomes]
rs6727919	0.88[ASW][hapmap];0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];0.85[MEX][hapmap];0.86[MKK][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6729266	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6732369	0.80[CHD][hapmap];0.84[GIH][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap]
rs6736153	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.96[TSI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6749237	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6750069	0.80[CEU][hapmap];0.81[JPT][hapmap]
rs6754779	0.87[AFR][1000 genomes]
rs6757131	0.80[CEU][hapmap];0.81[JPT][hapmap]
rs6759733	0.80[CEU][hapmap]
rs727470	0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs727471	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs732178	0.80[CEU][hapmap]
rs732179	0.80[CEU][hapmap]
rs732180	0.80[CEU][hapmap];0.82[GIH][hapmap];0.81[MEX][hapmap]
rs7557173	0.83[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7559074	0.92[ASN][1000 genomes]
rs7559340	0.87[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.82[YRI][hapmap];0.94[ASN][1000 genomes]
rs7566904	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.85[MEX][hapmap];0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7570876	0.86[JPT][hapmap];0.82[YRI][hapmap]
rs7579770	0.81[JPT][hapmap]
rs7580216	0.80[CEU][hapmap];0.82[GIH][hapmap];0.90[MEX][hapmap]
rs7593322	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7597032	0.81[JPT][hapmap]
rs7599657	0.92[ASN][1000 genomes]
rs7602651	0.94[ASW][hapmap];0.87[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];0.90[MEX][hapmap];0.85[MKK][hapmap];0.89[YRI][hapmap];0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs891432	0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs891433	0.83[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs893258	0.81[JPT][hapmap]
rs893259	0.81[JPT][hapmap];0.90[MEX][hapmap]
rs9309471	0.89[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs13400948	RAB11FIP5	cis	multi-tissue	Pritchard
rs13400948	ADD2	cis	parietal	SCAN
rs13400948	SFXN5	cis	cerebellum	SCAN
rs13400948	MXD1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:73249400-73290000	Weak transcription	HUVEC	blood vessel
2	chr2:73249600-73290000	Weak transcription	NHLF	lung
3	chr2:73256800-73290000	Weak transcription	HSMM	muscle
4	chr2:73259200-73291200	Weak transcription	Small Intestine	intestine
5	chr2:73262800-73290600	Weak transcription	NHEK	skin
6	chr2:73264200-73290600	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr2:73272600-73291200	Weak transcription	Fetal Heart	heart
8	chr2:73275800-73297000	Weak transcription	Pancreas	Pancrea
9	chr2:73277800-73290400	Weak transcription	HMEC	breast
10	chr2:73277800-73290800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr2:73277800-73291200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr2:73284200-73290000	Weak transcription	Hela-S3	cervix
13	chr2:73284600-73290000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr2:73284600-73290600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr2:73284600-73296600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr2:73284800-73290200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr2:73284800-73296400	Weak transcription	Fetal Kidney	kidney
18	chr2:73285000-73290000	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr2:73285000-73290000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr2:73285000-73290600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr2:73285000-73290600	Weak transcription	HSMMtube	muscle
22	chr2:73285000-73290800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr2:73285000-73291200	Weak transcription	Colon Smooth Muscle	Colon
24	chr2:73285000-73291200	Weak transcription	Fetal Muscle Trunk	muscle
25	chr2:73285000-73291200	Weak transcription	Lung	lung
26	chr2:73285000-73291200	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr2:73285000-73291200	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr2:73285000-73295600	Weak transcription	Primary B cells from cord blood	blood
29	chr2:73285000-73295800	Weak transcription	Rectal Smooth Muscle	rectum
30	chr2:73285000-73296000	Weak transcription	Adipose Nuclei	Adipose
31	chr2:73285000-73296000	Weak transcription	Gastric	stomach
32	chr2:73285000-73296000	Weak transcription	Thymus	Thymus
33	chr2:73285000-73296600	Weak transcription	Placenta	Placenta
34	chr2:73285000-73296600	Weak transcription	Ovary	ovary
35	chr2:73285200-73290000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr2:73285200-73290000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr2:73285200-73290600	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr2:73285200-73290600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr2:73285200-73290800	Weak transcription	Pancreatic Islets	Pancreatic Islet
40	chr2:73285200-73291000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr2:73285200-73295800	Weak transcription	Stomach Smooth Muscle	stomach
42	chr2:73285200-73296400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr2:73285400-73290000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr2:73285400-73290000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr2:73285400-73290800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr2:73285600-73290400	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr2:73285600-73290400	Weak transcription	Fetal Intestine Large	intestine
48	chr2:73285600-73290600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr2:73285600-73291400	Weak transcription	Duodenum Mucosa	Duodenum
50	chr2:73285600-73291800	Weak transcription	Fetal Thymus	thymus

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