Variant report

Variant	rs1864488
Chromosome Location	chr2:73339708-73339709
allele	C/T
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	ZNF143	chr2:73338927-73339908	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr2:73339437-73340770	A549	lung:	n/a	n/a
3	E2F6	chr2:73339292-73340802	K562	blood:	n/a	chr2:73339495-73339503 chr2:73340674-73340683 chr2:73340621-73340631 chr2:73339458-73339467
4	MAX	chr2:73338571-73340886	K562	blood:	n/a	chr2:73340580-73340589 chr2:73340579-73340590 chr2:73340580-73340589
5	MAZ	chr2:73337286-73342118	IMR90	lung:	n/a	chr2:73340580-73340589 chr2:73340579-73340590 chr2:73337639-73337648 chr2:73340580-73340589
6	MAZ	chr2:73339579-73339805	HepG2	liver:	n/a	n/a
7	POLR2A	chr2:73339578-73340780	HepG2	liver:	n/a	n/a
8	SMARCB1	chr2:73338108-73340874	Hela-S3	cervix:	n/a	n/a
9	GABPA	chr2:73339708-73340042	K562	blood:	n/a	n/a
10	RCOR1	chr2:73339317-73340882	K562	blood:	n/a	n/a
11	POLR2A	chr2:73339524-73340916	HEK293	kidney:	n/a	n/a
12	CTCF	chr2:73339560-73339710	SAEC	small airway:	n/a	n/a
13	CTCF	chr2:73339560-73339710	SK-N-SH_RA	brain:	n/a	n/a
14	ARID3A	chr2:73339592-73339786	HepG2	liver:	n/a	n/a
15	MXI1	chr2:73338627-73339712	Hela-S3	cervix:	n/a	n/a
16	POLR2A	chr2:73339655-73340047	U87	brain:	n/a	n/a
17	JUND	chr2:73339702-73340900	A549	lung:	n/a	chr2:73340572-73340581
18	EGR1	chr2:73339692-73339973	K562	blood:	n/a	n/a
19	CTBP2	chr2:73338937-73339750	H1-hESC	embryonic stem cell:	n/a	n/a
20	POLR2A	chr2:73338506-73340908	Hela-S3	cervix:	n/a	n/a
21	MAX	chr2:73338533-73341015	HepG2	liver:	n/a	chr2:73340580-73340589 chr2:73340579-73340590 chr2:73340580-73340589
22	MXI1	chr2:73337661-73341153	IMR90	lung:	n/a	chr2:73340581-73340590
23	MAX	chr2:73338310-73340969	HepG2	liver:	n/a	chr2:73340580-73340589 chr2:73340579-73340590 chr2:73340580-73340589
24	POLR2A	chr2:73338786-73340948	MCF10A-Er-Src	breast:	n/a	n/a
25	MXI1	chr2:73339349-73340868	HepG2	liver:	n/a	chr2:73340581-73340590
26	MYC	chr2:73338641-73339881	MCF10A-Er-Src	breast:	n/a	n/a
27	POLR2A	chr2:73339494-73340872	K562	blood:	n/a	n/a
28	MAX	chr2:73339163-73339831	SK-N-SH	brain:	n/a	n/a
29	E2F6	chr2:73338916-73339752	H1-hESC	embryonic stem cell:	n/a	chr2:73339495-73339503 chr2:73339458-73339467
30	HDAC2	chr2:73339191-73340052	HepG2	liver:	n/a	n/a
31	POLR2A	chr2:73339361-73339720	K562	blood:	n/a	n/a
32	ATF3	chr2:73339481-73339715	K562	blood:	n/a	n/a
33	CREB1	chr2:73339340-73340778	A549	lung:	n/a	n/a
34	MAX	chr2:73338342-73341046	HCT-116	colon:	n/a	chr2:73340580-73340589 chr2:73340579-73340590 chr2:73340580-73340589
35	MAX	chr2:73338801-73340872	H1-hESC	embryonic stem cell:	n/a	chr2:73340580-73340589 chr2:73340579-73340590 chr2:73340580-73340589
36	ZBTB7A	chr2:73339186-73340933	ECC-1	luminal epithelium:	n/a	chr2:73339459-73339468 chr2:73340215-73340222
37	MAX	chr2:73338845-73339861	H1-hESC	embryonic stem cell:	n/a	n/a
38	TAF1	chr2:73339465-73340407	HepG2	liver:	n/a	n/a
39	MAX	chr2:73338590-73339954	MCF-7	breast:	n/a	n/a
40	CREB1	chr2:73338062-73340963	HepG2	liver:	n/a	n/a
41	POLR2A	chr2:73339336-73340489	H1-neurons	neurons:	n/a	n/a
42	UBTF	chr2:73338443-73340834	K562	blood:	n/a	n/a
43	MAX	chr2:73338515-73341035	A549	lung:	n/a	chr2:73340580-73340589 chr2:73340579-73340590 chr2:73340580-73340589
44	POLR2A	chr2:73339406-73340760	A549	lung:	n/a	n/a
45	BACH1	chr2:73339539-73339872	H1-hESC	embryonic stem cell:	n/a	n/a
46	MAX	chr2:73338623-73340897	A549	lung:	n/a	chr2:73340580-73340589 chr2:73340579-73340590 chr2:73340580-73340589
47	TAF1	chr2:73339354-73340735	HepG2	liver:	n/a	n/a
48	SIN3AK20	chr2:73339544-73340081	PANC-1	pancreas:	n/a	n/a
49	SIN3A	chr2:73338480-73340759	H1-hESC	embryonic stem cell:	n/a	chr2:73338958-73338969 chr2:73339396-73339410
50	TCF12	chr2:73337954-73339898	A549	lung:	n/a	chr2:73339022-73339029

No.	Distal block	Cell Line	Cell type
1	chr2:73297299..73299304-chr2:73339003..73341312,3	MCF-7	breast:
2	chr2:73337867..73339816-chr2:73350346..73352327,2	K562	blood:
3	chr2:73296300..73298115-chr2:73338664..73340371,2	K562	blood:
4	chr2:73336661..73339816-chr2:73350346..73353019,4	K562	blood:
5	chr12:72056797..72057679-chr2:73339707..73340467,3	Hela-S3	cervix:
6	chr2:73338342..73340040-chr2:73341941..73344372,2	MCF-7	breast:
7	chr2:73339424..73339924-chr7:148987693..148988217,2	NB4	blood:

Variant related genes	Relation type
ENSG00000272702	TF binding region
ENSG00000133858	Chromatin interaction
ENSG00000144040	Chromatin interaction

Extended variants
information (count: 100 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:97)

rs_ID	r²[population]
rs10166220	0.91[JPT][hapmap]
rs10167566	0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs10174548	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10176939	0.86[JPT][hapmap]
rs10177159	0.81[JPT][hapmap]
rs10180720	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]
rs10180995	0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap];0.94[ASN][1000 genomes]
rs10189744	0.91[JPT][hapmap]
rs10190861	0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs10192077	0.81[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap]
rs10197305	0.86[JPT][hapmap]
rs10203608	0.90[ASN][1000 genomes]
rs1046186	0.91[ASN][1000 genomes]
rs10865396	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11126389	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11686557	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11885522	0.96[ASN][1000 genomes]
rs12104691	0.94[ASN][1000 genomes]
rs12233055	0.81[JPT][hapmap];0.86[MEX][hapmap]
rs12614059	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13018842	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13019020	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13385994	0.91[ASN][1000 genomes]
rs13388404	0.91[JPT][hapmap]
rs13391532	0.96[ASN][1000 genomes]
rs13393567	0.89[ASN][1000 genomes]
rs13400920	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]
rs13400948	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]
rs13403757	0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs13403781	0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs13407719	0.89[ASN][1000 genomes]
rs13416407	0.95[CHB][hapmap];0.86[JPT][hapmap];0.94[ASN][1000 genomes]
rs13427947	0.91[ASN][1000 genomes]
rs1370383	0.86[MEX][hapmap]
rs1430349	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.99[ASN][1000 genomes]
rs1430350	0.96[ASN][1000 genomes]
rs1430351	0.96[ASN][1000 genomes]
rs17008571	0.86[JPT][hapmap]
rs17008611	0.81[JPT][hapmap]
rs17008631	0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1992133	0.95[CHB][hapmap];0.98[CHD][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs2421098	0.82[CHD][hapmap];0.91[JPT][hapmap]
rs35131031	0.88[ASN][1000 genomes]
rs3813222	0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs3813223	0.91[ASN][1000 genomes]
rs3901273	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4144837	0.91[JPT][hapmap]
rs4514897	0.81[CHD][hapmap];0.91[JPT][hapmap]
rs4591365	0.96[ASN][1000 genomes]
rs55894650	0.92[ASN][1000 genomes]
rs57536428	0.88[ASN][1000 genomes]
rs57701326	0.96[ASN][1000 genomes]
rs57726945	0.99[ASN][1000 genomes]
rs57937746	0.88[ASN][1000 genomes]
rs6546796	0.81[JPT][hapmap];0.91[MEX][hapmap]
rs6546797	0.81[JPT][hapmap];0.86[MEX][hapmap]
rs6546800	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6546801	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6709938	0.86[JPT][hapmap]
rs6710739	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]
rs6710755	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6711891	0.86[JPT][hapmap];0.86[MEX][hapmap]
rs6712925	0.94[ASN][1000 genomes]
rs6719333	0.91[JPT][hapmap]
rs6720817	0.90[ASN][1000 genomes]
rs6726940	0.81[JPT][hapmap]
rs6727919	0.91[CHB][hapmap];0.98[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.82[TSI][hapmap];0.94[ASN][1000 genomes]
rs6729266	0.95[CHB][hapmap];0.98[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.90[ASN][1000 genomes]
rs6732369	0.91[JPT][hapmap];0.91[MEX][hapmap]
rs6736153	0.95[CHB][hapmap];0.98[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6749237	0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs6750069	0.86[JPT][hapmap]
rs6757131	0.86[JPT][hapmap]
rs6759733	0.80[JPT][hapmap];0.81[MEX][hapmap]
rs727470	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs727471	0.94[ASN][1000 genomes]
rs732179	0.81[JPT][hapmap]
rs732180	0.80[JPT][hapmap];0.86[MEX][hapmap]
rs7557173	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.94[ASN][1000 genomes]
rs7559074	0.96[ASN][1000 genomes]
rs7559340	0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.94[ASN][1000 genomes]
rs7566904	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]
rs7567413	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7570459	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7570876	0.91[JPT][hapmap]
rs7579770	0.86[JPT][hapmap]
rs7580216	0.81[JPT][hapmap];0.86[MEX][hapmap]
rs7593322	0.96[ASN][1000 genomes]
rs7596830	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7597032	0.86[JPT][hapmap]
rs7599657	0.96[ASN][1000 genomes]
rs7602651	1.00[CHB][hapmap];0.98[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.82[TSI][hapmap];0.99[ASN][1000 genomes]
rs891432	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs891433	0.95[CHB][hapmap];0.98[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.81[TSI][hapmap];0.94[ASN][1000 genomes]
rs893258	0.86[JPT][hapmap]
rs893259	0.86[JPT][hapmap];0.95[MEX][hapmap]
rs9309471	0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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
3	esv3329435	chr2:73338669-73341217	Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1864488	SFXN5	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:73337200-73340000	Flanking Active TSS	Stomach Smooth Muscle	stomach
2	chr2:73337800-73340000	Flanking Active TSS	Colonic Mucosa	Colon
3	chr2:73338000-73340800	Active TSS	Aorta	Aorta
4	chr2:73338000-73341200	Active TSS	Pancreatic Islets	Pancreatic Islet
5	chr2:73338200-73339800	Flanking Active TSS	Adipose Nuclei	Adipose
6	chr2:73338200-73339800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
7	chr2:73338200-73339800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
8	chr2:73338200-73340800	Active TSS	Gastric	stomach
9	chr2:73338200-73341000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr2:73338200-73341000	Active TSS	HSMM	muscle
11	chr2:73338400-73339800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr2:73338400-73339800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr2:73338400-73339800	Flanking Active TSS	Liver	Liver
14	chr2:73338400-73340000	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
15	chr2:73338400-73340800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr2:73338400-73341200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr2:73338600-73339800	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
18	chr2:73338600-73339800	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
19	chr2:73338600-73339800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr2:73338600-73340000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr2:73338600-73340400	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
22	chr2:73338600-73340600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr2:73338600-73340800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr2:73338600-73340800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr2:73338600-73340800	Active TSS	HUES6 Cell Line	embryonic stem cell
26	chr2:73338600-73340800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr2:73338600-73340800	Active TSS	Esophagus	oesophagus
28	chr2:73338600-73340800	Active TSS	Left Ventricle	heart
29	chr2:73338600-73340800	Active TSS	Placenta Amnion	Placenta Amnion
30	chr2:73338600-73340800	Active TSS	Right Atrium	heart
31	chr2:73338600-73340800	Active TSS	Hela-S3	cervix
32	chr2:73338600-73340800	Active TSS	NHDF-Ad	bronchial
33	chr2:73338600-73340800	Active TSS	NHEK	skin
34	chr2:73338600-73340800	Active TSS	NHLF	lung
35	chr2:73338600-73341000	Active TSS	ES-I3 Cell Line	embryonic stem cell
36	chr2:73338600-73341000	Active TSS	H9 Cell Line	embryonic stem cell
37	chr2:73338600-73341000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr2:73338600-73341000	Active TSS	Breast Myoepithelial Primary Cells	Breast
39	chr2:73338600-73341000	Active TSS	Right Ventricle	heart
40	chr2:73338600-73341000	Active TSS	HSMMtube	muscle
41	chr2:73338600-73341200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
42	chr2:73338600-73341200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr2:73338800-73339800	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
44	chr2:73338800-73340400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr2:73338800-73340400	Active TSS	Osteobl	bone
46	chr2:73338800-73340800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr2:73338800-73340800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr2:73338800-73340800	Active TSS	Fetal Kidney	kidney
49	chr2:73338800-73341000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr2:73338800-73341400	Active TSS	A549	lung

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