Variant report

Variant	rs2295366
Chromosome Location	chr1:173825692-173825693
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:173823430..173826161-chr1:173990406..173993214,2	MCF-7	breast:
2	chr1:173791743..173795924-chr1:173822974..173827118,6	K562	blood:
3	chr1:173808404..173810597-chr1:173824341..173827364,3	MCF-7	breast:
4	chr1:173457080..173459531-chr1:173825329..173828115,2	K562	blood:
5	chr1:173793044..173798309-chr1:173822396..173826299,5	K562	blood:

Variant related genes	Relation type
ENSG00000120334	Chromatin interaction
ENSG00000117593	Chromatin interaction
ENSG00000224977	Chromatin interaction
ENSG00000135870	Chromatin interaction

Extended variants
information (count: 89 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10912670	0.85[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs10912671	0.95[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.97[TSI][hapmap];0.88[ASN][1000 genomes]
rs12082131	0.81[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs12086229	0.90[ASN][1000 genomes]
rs12561931	0.95[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.83[TSI][hapmap];0.93[ASN][1000 genomes]
rs12564699	0.90[ASN][1000 genomes]
rs12565915	0.93[ASN][1000 genomes]
rs12566945	0.90[ASN][1000 genomes]
rs1322774	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16846439	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1799876	0.85[MEX][hapmap]
rs1951625	0.94[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];0.94[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2067079	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2144708	0.95[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2208850	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2227588	0.85[CHB][hapmap]
rs2227612	0.85[CHB][hapmap]
rs2273366	0.95[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.85[TSI][hapmap];0.94[ASN][1000 genomes]
rs2281486	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28804123	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3791020	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs45467799	0.90[ASN][1000 genomes]
rs4558043	0.90[ASN][1000 genomes]
rs4652283	0.85[CHB][hapmap]
rs4652298	0.85[CHB][hapmap]
rs4652328	0.85[CHB][hapmap]
rs55633896	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55829688	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56019876	0.94[ASN][1000 genomes]
rs56048122	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56138893	0.85[ASN][1000 genomes]
rs56369162	0.93[ASN][1000 genomes]
rs56928371	0.93[ASN][1000 genomes]
rs57799150	0.94[ASN][1000 genomes]
rs58287165	0.85[ASN][1000 genomes]
rs5878	0.85[MEX][hapmap]
rs58825445	0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs59858609	0.85[ASN][1000 genomes]
rs60264384	0.93[ASN][1000 genomes]
rs61826805	0.85[ASN][1000 genomes]
rs61826806	0.85[ASN][1000 genomes]
rs61826809	0.85[ASN][1000 genomes]
rs61826810	0.85[ASN][1000 genomes]
rs61826812	0.88[ASN][1000 genomes]
rs61826813	0.88[ASN][1000 genomes]
rs61826821	0.94[ASN][1000 genomes]
rs61826856	0.94[ASN][1000 genomes]
rs61826857	0.92[ASN][1000 genomes]
rs61827860	0.94[ASN][1000 genomes]
rs61827861	0.94[ASN][1000 genomes]
rs61827863	0.93[ASN][1000 genomes]
rs61827865	0.91[ASN][1000 genomes]
rs61827867	0.93[ASN][1000 genomes]
rs61827870	0.93[ASN][1000 genomes]
rs61827876	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61827877	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61827881	0.94[ASN][1000 genomes]
rs61827925	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6413827	0.94[ASW][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];0.84[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs6425253	0.81[ASN][1000 genomes]
rs6425258	0.95[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.83[TSI][hapmap];0.93[ASN][1000 genomes]
rs6425261	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6663875	0.81[MEX][hapmap]
rs6668702	0.90[ASN][1000 genomes]
rs6673175	0.81[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs6674381	0.90[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6681766	0.85[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs6691001	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6696680	0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7514556	0.95[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs7515721	0.95[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7521884	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7530546	0.94[ASN][1000 genomes]
rs7546048	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7548171	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7552741	0.95[CHB][hapmap];0.95[JPT][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs941989	0.85[MEX][hapmap]
rs9425416	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9425430	0.81[MEX][hapmap]
rs9425431	0.85[CHB][hapmap]
rs9425433	0.85[CHB][hapmap]
rs9425745	0.94[ASW][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];0.84[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9425756	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9425766	0.84[MEX][hapmap]
rs9660881	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012384	chr1:173614816-173974426	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	294 gene(s)	inside rSNPs	diseases
2	nsv831926	chr1:173702403-173894667	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	291 gene(s)	inside rSNPs	diseases
3	esv2757761	chr1:173810642-173955943	Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	264 gene(s)	inside rSNPs	diseases
4	esv2758978	chr1:173810642-173955943	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	264 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2295366	RABGAP1L	cis	parietal	SCAN
rs2295366	SLC9A11	cis	parietal	SCAN
rs2295366	PRDX6	cis	parietal	SCAN
rs2295366	DARS2	cis	Muscle Skeletal	GTEx
rs2295366	DARS2	cis	cerebellum	SCAN
rs2295366	SERPINC1	cis	multi-tissue	Pritchard
rs2295366	TNN	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:173794400-173832800	Weak transcription	Fetal Heart	heart
2	chr1:173794600-173832000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr1:173794600-173832000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr1:173794600-173832600	Weak transcription	Brain Substantia Nigra	brain
5	chr1:173794600-173833800	Weak transcription	Stomach Mucosa	stomach
6	chr1:173794800-173834000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr1:173795000-173826200	Weak transcription	Psoas Muscle	Psoas
8	chr1:173795000-173834600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr1:173797200-173828400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr1:173799600-173828800	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr1:173803000-173826600	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr1:173809800-173831800	Weak transcription	Colonic Mucosa	Colon
13	chr1:173811200-173829200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr1:173813200-173831800	Weak transcription	Right Ventricle	heart
15	chr1:173813200-173832000	Weak transcription	Small Intestine	intestine
16	chr1:173813400-173831000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr1:173814600-173826400	Weak transcription	Hela-S3	cervix
18	chr1:173815000-173826000	Weak transcription	Esophagus	oesophagus
19	chr1:173818200-173831600	Weak transcription	Fetal Brain Male	brain
20	chr1:173818400-173829000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr1:173818400-173829800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr1:173818600-173829600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
23	chr1:173818600-173830200	Strong transcription	Primary T cells fromperipheralblood	blood
24	chr1:173818600-173834800	Strong transcription	Fetal Muscle Leg	muscle
25	chr1:173818600-173834800	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr1:173818800-173827200	Strong transcription	Primary T cells from cord blood	blood
27	chr1:173818800-173827800	Strong transcription	Dnd41	blood
28	chr1:173819200-173828200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr1:173819200-173833200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr1:173819200-173833800	Strong transcription	Primary T helper cells fromperipheralblood	blood
31	chr1:173819200-173834000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr1:173819400-173827600	Strong transcription	HMEC	breast
33	chr1:173819400-173829800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr1:173819400-173832000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr1:173819400-173834800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr1:173819600-173830000	Weak transcription	Right Atrium	heart
37	chr1:173819600-173834000	Strong transcription	Fetal Thymus	thymus
38	chr1:173819600-173835600	Strong transcription	Fetal Muscle Trunk	muscle
39	chr1:173819800-173827600	Strong transcription	Duodenum Mucosa	Duodenum
40	chr1:173820400-173828200	Strong transcription	Adipose Nuclei	Adipose
41	chr1:173820400-173828600	Strong transcription	Primary neutrophils fromperipheralblood	blood
42	chr1:173820600-173827400	Strong transcription	HSMM	muscle
43	chr1:173820600-173827600	Strong transcription	K562	blood
44	chr1:173820600-173828200	Strong transcription	Primary T helper cells PMA-I stimulated	--
45	chr1:173820600-173833800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr1:173820600-173834000	Strong transcription	Primary B cells from peripheral blood	blood
47	chr1:173821000-173828600	Strong transcription	Skeletal Muscle Female	skeletal muscle
48	chr1:173821000-173834000	Strong transcription	Liver	Liver
49	chr1:173821000-173834000	Strong transcription	Rectal Mucosa Donor 31	rectum
50	chr1:173821200-173828000	Strong transcription	Aorta	Aorta

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