Variant report

Variant	rs7514280
Chromosome Location	chr1:93320869-93320870
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	chr1:93305489..93308255-chr1:93319835..93322646,2	K562	blood:

Variant related genes	Relation type
ENSG00000207523	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10874745	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11164803	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11164814	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11164820	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.83[TSI][hapmap]
rs11164825	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11164857	1.00[CHB][hapmap]
rs11577426	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11578004	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11582791	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11586089	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11586570	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11800409	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11800771	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11800848	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11803097	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11810217	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12062315	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12066638	0.86[MKK][hapmap]
rs12081675	1.00[JPT][hapmap]
rs12082659	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12726286	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12728322	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12731107	1.00[JPT][hapmap]
rs12738654	0.81[EUR][1000 genomes]
rs12743005	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12746893	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12746956	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12747275	1.00[JPT][hapmap]
rs12749786	1.00[CHB][hapmap]
rs12750269	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17381426	1.00[CHB][hapmap]
rs1854797	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2391177	0.84[MKK][hapmap]
rs2811600	0.80[MKK][hapmap]
rs2893226	0.91[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.97[TSI][hapmap];0.80[YRI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34041593	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34098754	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34168045	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34202284	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs34244251	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35031391	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35051335	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35183060	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58270016	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6604026	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.89[TSI][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66525381	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6657809	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6687931	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6698233	0.82[MKK][hapmap]
rs71652510	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7521417	0.90[CEU][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7554594	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[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	nsv1008602	chr1:93176811-93640808	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv508393	chr1:93290513-93344924	Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7514280	FAM69A	cis	Artery Tibial	GTEx
rs7514280	HFM1	cis	parietal	SCAN

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:93304400-93349000	Weak transcription	Aorta	Aorta
2	chr1:93306800-93324800	Weak transcription	Pancreas	Pancrea
3	chr1:93307000-93324800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr1:93308000-93323400	Weak transcription	Small Intestine	intestine
5	chr1:93308000-93324600	Weak transcription	Psoas Muscle	Psoas
6	chr1:93309400-93324800	Weak transcription	NHDF-Ad	bronchial
7	chr1:93309600-93324800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr1:93309800-93324200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr1:93309800-93324400	Weak transcription	A549	lung
10	chr1:93309800-93324400	Weak transcription	Osteobl	bone
11	chr1:93309800-93342400	Weak transcription	NHLF	lung
12	chr1:93310000-93324200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr1:93310000-93324200	Weak transcription	Brain Substantia Nigra	brain
14	chr1:93310000-93324800	Weak transcription	HSMMtube	muscle
15	chr1:93310200-93323600	Weak transcription	HepG2	liver
16	chr1:93310200-93324600	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr1:93310400-93324200	Weak transcription	Fetal Thymus	thymus
18	chr1:93310400-93324400	Weak transcription	Stomach Smooth Muscle	stomach
19	chr1:93310400-93324800	Weak transcription	Left Ventricle	heart
20	chr1:93311000-93323200	Weak transcription	Liver	Liver
21	chr1:93311600-93324200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr1:93313600-93324200	Weak transcription	Brain Cingulate Gyrus	brain
23	chr1:93314400-93338000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr1:93316000-93342800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr1:93316200-93322800	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr1:93316200-93324200	Weak transcription	Thymus	Thymus
27	chr1:93316200-93324400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr1:93316200-93324800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr1:93316200-93338200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr1:93316200-93338400	Weak transcription	Fetal Stomach	stomach
31	chr1:93316600-93324200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr1:93316600-93324200	Weak transcription	Primary T helper cells PMA-I stimulated	--
33	chr1:93316800-93323400	Weak transcription	Primary T helper cells fromperipheralblood	blood
34	chr1:93316800-93324600	Weak transcription	Colon Smooth Muscle	Colon
35	chr1:93317400-93324600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr1:93318200-93324600	Weak transcription	NHEK	skin
37	chr1:93318400-93323800	Weak transcription	Dnd41	blood
38	chr1:93318600-93324200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr1:93318600-93324200	Weak transcription	Brain Anterior Caudate	brain
40	chr1:93318600-93338200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr1:93319000-93323800	Weak transcription	Primary T cells from cord blood	blood
42	chr1:93319200-93321600	Enhancers	Placenta	Placenta
43	chr1:93319200-93324200	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr1:93319400-93327800	Weak transcription	Primary B cells from cord blood	blood
45	chr1:93320200-93323200	Weak transcription	Fetal Intestine Large	intestine
46	chr1:93320200-93323600	Weak transcription	Brain Angular Gyrus	brain
47	chr1:93320200-93324400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
48	chr1:93320200-93324600	Weak transcription	Brain Hippocampus Middle	brain
49	chr1:93320400-93321200	ZNF genes & repeats	Primary B cells from peripheral blood	blood
50	chr1:93320400-93323000	Weak transcription	Duodenum Mucosa	Duodenum

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