Variant report

Variant	rs35183060
Chromosome Location	chr1:93346928-93346929
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10874745	0.96[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	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap]
rs11164825	0.93[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	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11586089	0.91[AMR][1000 genomes];0.88[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];0.95[MKK][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11800409	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	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12081675	1.00[JPT][hapmap]
rs12082659	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12726286	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[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];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12731107	1.00[JPT][hapmap]
rs12738654	0.87[EUR][1000 genomes]
rs12743005	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12746893	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12746956	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12747275	1.00[JPT][hapmap]
rs12749786	1.00[CHB][hapmap]
rs12750269	0.95[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];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2255723	0.92[MKK][hapmap]
rs2263247	0.91[MKK][hapmap]
rs2481713	0.92[MKK][hapmap]
rs2811593	0.92[MKK][hapmap]
rs2893226	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34041593	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34098754	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34168045	0.87[EUR][1000 genomes]
rs34202284	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs34244251	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35031391	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35051335	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58270016	0.91[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];0.89[TSI][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66525381	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6657809	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6687931	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71652510	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7514280	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]
rs7521417	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.94[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7538968	0.91[YRI][hapmap]
rs7554594	0.92[EUR][1000 genomes];1.00[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	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs35183060	FAM69A	cis	Artery Tibial	GTEx
rs35183060	FAM69A	cis	parietal	SCAN
rs35183060	KIAA1107	cis	cerebellum	SCAN

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:93304400-93349000	Weak transcription	Aorta	Aorta
2	chr1:93325200-93348400	Weak transcription	NHEK	skin
3	chr1:93333000-93348600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr1:93335800-93348400	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr1:93336400-93348800	Weak transcription	Left Ventricle	heart
6	chr1:93336600-93349200	Weak transcription	HepG2	liver
7	chr1:93337000-93348400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr1:93338800-93347800	Weak transcription	HMEC	breast
9	chr1:93338800-93348200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr1:93338800-93348400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr1:93339000-93348200	Weak transcription	Monocytes-CD14+_RO01746	blood
12	chr1:93339000-93352600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr1:93340800-93348800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr1:93340800-93351600	Weak transcription	Small Intestine	intestine
15	chr1:93343400-93348400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr1:93343800-93348000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr1:93343800-93348400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr1:93343800-93348400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr1:93343800-93348400	Weak transcription	Osteobl	bone
20	chr1:93343800-93348600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr1:93344000-93348000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr1:93344000-93348400	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr1:93344000-93348400	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr1:93344000-93348400	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr1:93344200-93348000	Weak transcription	Primary B cells from cord blood	blood
26	chr1:93344600-93351400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr1:93345200-93348400	Weak transcription	GM12878-XiMat	blood
28	chr1:93345600-93348000	Weak transcription	Primary T helper cells fromperipheralblood	blood
29	chr1:93345600-93348200	Weak transcription	Primary B cells from peripheral blood	blood
30	chr1:93345600-93348200	Weak transcription	Fetal Thymus	thymus
31	chr1:93345600-93348600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr1:93345600-93350000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
33	chr1:93345800-93347000	Weak transcription	Primary T cells from cord blood	blood
34	chr1:93345800-93347000	Weak transcription	Primary T cells fromperipheralblood	blood
35	chr1:93345800-93347200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
36	chr1:93345800-93347200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
37	chr1:93345800-93347800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr1:93345800-93348000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr1:93345800-93348000	Weak transcription	Thymus	Thymus
40	chr1:93345800-93348400	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr1:93345800-93348400	Weak transcription	Brain Anterior Caudate	brain
42	chr1:93345800-93348400	Weak transcription	Brain Cingulate Gyrus	brain
43	chr1:93345800-93348400	Weak transcription	Brain Substantia Nigra	brain
44	chr1:93346200-93348000	Weak transcription	Dnd41	blood
45	chr1:93346400-93348000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr1:93346800-93347200	Enhancers	Brain Inferior Temporal Lobe	brain
47	chr1:93346800-93347400	Enhancers	Primary T helper cells PMA-I stimulated	--
48	chr1:93346800-93347400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr1:93346800-93347400	Enhancers	Brain Hippocampus Middle	brain

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