Variant report

Variant	rs6667614
Chromosome Location	chr1:59001300-59001301
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:58993368..58995087-chr1:58998103..59001309,3	K562	blood:
2	chr1:58992969..58995087-chr1:58998392..59001677,3	K562	blood:
3	chr1:58999840..59003717-chr1:59009218..59013187,5	K562	blood:
4	chr1:59000333..59003093-chr1:59009787..59012199,2	MCF-7	breast:
5	chr1:59000599..59004010-chr1:59008365..59012989,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000162600	Chromatin interaction
ENSG00000173406	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10789063	0.85[ASN][1000 genomes]
rs10789067	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10889098	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1114660	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11207236	0.83[ASN][1000 genomes]
rs11207237	0.89[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11207240	0.83[ASN][1000 genomes]
rs1121422	0.87[ASN][1000 genomes]
rs11581395	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.82[TSI][hapmap];0.87[ASN][1000 genomes]
rs12030713	0.88[ASW][hapmap];0.86[MEX][hapmap];0.80[TSI][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12088149	0.83[ASN][1000 genomes]
rs12124662	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.82[TSI][hapmap];0.83[ASN][1000 genomes]
rs1388981	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1775002	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs232822	0.82[ASN][1000 genomes]
rs232826	1.00[CHB][hapmap];0.92[JPT][hapmap];0.82[ASN][1000 genomes]
rs232827	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs232830	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28529311	0.83[ASN][1000 genomes]
rs3087585	0.86[MEX][hapmap];0.80[TSI][hapmap]
rs338224	0.83[ASN][1000 genomes]
rs338225	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.93[MEX][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];0.91[YRI][hapmap];0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs3551	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs486463	0.88[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.80[TSI][hapmap];0.85[ASN][1000 genomes]
rs4912195	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.82[TSI][hapmap];0.87[ASN][1000 genomes]
rs4912344	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs525929	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs602579	0.82[ASW][hapmap];0.86[MEX][hapmap]
rs6587818	0.87[ASN][1000 genomes]
rs6587819	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs6587828	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs659061	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs6656025	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.93[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6667703	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.95[YRI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6687324	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.82[TSI][hapmap];0.83[ASN][1000 genomes]
rs672359	0.87[ASN][1000 genomes]
rs67639631	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7517424	0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7520008	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7536230	0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.82[TSI][hapmap];0.87[ASN][1000 genomes]
rs7544032	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7547036	0.88[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.93[MEX][hapmap];0.82[TSI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7554278	0.83[ASN][1000 genomes]
rs9660901	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[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	nsv1003930	chr1:58930444-59157038	Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv998092	chr1:58978327-59002319	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs6667614	OMA1	cis	multi-tissue	Pritchard
rs6667614	DAB1	cis	cerebellum	SCAN
rs6667614	TACSTD2	cis	Thyroid	GTEx
rs6667614	MYSM1	cis	parietal	SCAN
rs6667614	OMA1	cis	parietal	SCAN
rs6667614	DAB1///OMA1	Cis_1M	lymphoblastoid	RTeQTL
rs6667614	OMA1	cis	lymphoblastoid	seeQTL
rs6667614	TACSTD2	cis	multi-tissue	Pritchard
rs6667614	OMA1	cis	cerebellum	SCAN
rs6667614	DAB1	cis	parietal	SCAN

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:58931200-59010800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr1:58966600-59010600	Weak transcription	Placenta	Placenta
3	chr1:58967600-59010600	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr1:58974800-59005000	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr1:58974800-59010800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr1:58974800-59011800	Weak transcription	Spleen	Spleen
7	chr1:58975000-59010600	Weak transcription	Stomach Smooth Muscle	stomach
8	chr1:58975000-59010800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr1:58977200-59005000	Weak transcription	Rectal Smooth Muscle	rectum
10	chr1:58977200-59010800	Weak transcription	Brain Angular Gyrus	brain
11	chr1:58977200-59011400	Weak transcription	Ovary	ovary
12	chr1:58977400-59005400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr1:58977400-59008600	Weak transcription	Brain Anterior Caudate	brain
14	chr1:58977400-59010400	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr1:58977400-59010600	Weak transcription	Aorta	Aorta
16	chr1:58977400-59010600	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr1:58977400-59010600	Weak transcription	Psoas Muscle	Psoas
18	chr1:58977400-59011400	Weak transcription	Left Ventricle	heart
19	chr1:58977400-59011400	Weak transcription	Lung	lung
20	chr1:58977600-59011000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr1:58978200-59010200	Weak transcription	Dnd41	blood
22	chr1:58979000-59005400	Weak transcription	Duodenum Mucosa	Duodenum
23	chr1:58979000-59011400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr1:58982200-59008200	Weak transcription	Brain Substantia Nigra	brain
25	chr1:58985200-59010600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr1:58985800-59010400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr1:58985800-59010600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr1:58989200-59004600	Weak transcription	Colon Smooth Muscle	Colon
29	chr1:58989200-59010600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
30	chr1:58989400-59010600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr1:58990800-59008200	Weak transcription	Brain Hippocampus Middle	brain
32	chr1:58990800-59011000	Weak transcription	Primary neutrophils fromperipheralblood	blood
33	chr1:58991400-59003800	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr1:58992400-59003400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr1:58992400-59010800	Weak transcription	Adipose Nuclei	Adipose
36	chr1:58993000-59001800	Weak transcription	Primary T helper cells fromperipheralblood	blood
37	chr1:58993000-59002200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr1:58993000-59004400	Weak transcription	Primary T cells fromperipheralblood	blood
39	chr1:58993000-59008400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr1:58993000-59010400	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr1:58993000-59010600	Weak transcription	Liver	Liver
42	chr1:58994200-59011000	Weak transcription	HSMM	muscle
43	chr1:58994400-59001600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr1:58994400-59010800	Weak transcription	NHEK	skin
45	chr1:58994600-59005000	Weak transcription	Fetal Lung	lung
46	chr1:58994600-59010600	Weak transcription	NHDF-Ad	bronchial
47	chr1:58995000-59004600	Weak transcription	Fetal Intestine Large	intestine
48	chr1:58995000-59004600	Weak transcription	Fetal Intestine Small	intestine
49	chr1:58995000-59010600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr1:58995200-59005000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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