Variant report

Variant	rs12085083
Chromosome Location	chr1:173408317-173408318
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:173403035..173408326-chr1:173791459..173795185,5	K562	blood:
2	chr1:173406280..173410007-chr1:173444433..173448102,3	MCF-7	breast:
3	chr1:173405237..173408410-chr1:173408631..173411366,3	K562	blood:
4	chr1:173398890..173402305-chr1:173404603..173408427,6	K562	blood:
5	chr1:173405257..173406898-chr1:173407237..173410019,2	K562	blood:
6	chr1:173407532..173410194-chr1:173412621..173414388,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000117593	Chromatin interaction
ENSG00000117592	Chromatin interaction
ENSG00000203739	Chromatin interaction
ENSG00000120334	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10912614	0.89[YRI][hapmap]
rs11800778	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11809166	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11811598	0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12075952	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12562415	0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34619706	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35263596	0.83[ASN][1000 genomes]
rs3934577	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55741047	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55816799	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57231379	0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57262055	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57951216	0.83[ASN][1000 genomes]
rs59834293	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60302114	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60587131	0.83[ASN][1000 genomes]
rs60969203	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61061894	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61261546	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6678064	0.93[CHB][hapmap];0.83[CHD][hapmap];0.90[TSI][hapmap]
rs6700269	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6700499	0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6702339	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72726915	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72726936	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72726946	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72726948	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72726949	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs74126390	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7529959	0.82[MKK][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes]
rs7534736	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7555324	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[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	nsv831915	chr1:173268424-173482157	Flanking Active TSS Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12085083	dJ383J4.3	cis	multi-tissue	Pritchard
rs12085083	FASLG	cis	cerebellum	SCAN
rs12085083	RABGAP1L	Cis_1M	lymphoblastoid	RTeQTL
rs12085083	TNFSF18	cis	parietal	SCAN
rs12085083		cis	Lymphoblastoid	GTEx

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:173376200-173429000	Weak transcription	Gastric	stomach
2	chr1:173387600-173429000	Weak transcription	Lung	lung
3	chr1:173391800-173429000	Weak transcription	Ovary	ovary
4	chr1:173399400-173408600	Weak transcription	Aorta	Aorta
5	chr1:173399400-173410000	Weak transcription	Primary T cells fromperipheralblood	blood
6	chr1:173399400-173410800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr1:173399400-173410800	Weak transcription	Pancreas	Pancrea
8	chr1:173399400-173414400	Weak transcription	Spleen	Spleen
9	chr1:173399400-173424200	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr1:173399600-173408600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr1:173399600-173412800	Weak transcription	Thymus	Thymus
12	chr1:173399800-173413000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr1:173399800-173413800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr1:173399800-173415400	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr1:173399800-173415600	Weak transcription	Liver	Liver
16	chr1:173400200-173421000	Weak transcription	Psoas Muscle	Psoas
17	chr1:173400200-173422800	Weak transcription	NH-A	brain
18	chr1:173400400-173429000	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr1:173400600-173413000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr1:173400600-173413600	Weak transcription	Primary T helper cells fromperipheralblood	blood
21	chr1:173400600-173413800	Weak transcription	Primary T helper cells PMA-I stimulated	--
22	chr1:173400600-173428800	Weak transcription	Fetal Stomach	stomach
23	chr1:173400800-173408600	Weak transcription	Primary monocytes fromperipheralblood	blood
24	chr1:173400800-173410800	Weak transcription	Primary hematopoietic stem cells	blood
25	chr1:173400800-173410800	Weak transcription	Brain Angular Gyrus	brain
26	chr1:173400800-173411200	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr1:173400800-173412600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr1:173400800-173413400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr1:173400800-173413800	Weak transcription	Primary B cells from peripheral blood	blood
30	chr1:173400800-173413800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr1:173400800-173413800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr1:173400800-173413800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr1:173400800-173414000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr1:173400800-173414200	Weak transcription	Fetal Muscle Trunk	muscle
35	chr1:173400800-173420600	Weak transcription	Hela-S3	cervix
36	chr1:173400800-173421000	Weak transcription	Colon Smooth Muscle	Colon
37	chr1:173400800-173422800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr1:173400800-173429000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr1:173400800-173429000	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr1:173401000-173408600	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr1:173401000-173415600	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr1:173401000-173418000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr1:173401000-173421000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr1:173401000-173421000	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr1:173401000-173422800	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr1:173401000-173428800	Weak transcription	Brain Hippocampus Middle	brain
47	chr1:173401000-173429000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr1:173401000-173429000	Weak transcription	Left Ventricle	heart
49	chr1:173401200-173408800	Weak transcription	HUES6 Cell Line	embryonic stem cell
50	chr1:173401200-173410400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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