Variant report

Variant	rs12120764
Chromosome Location	chr1:170514229-170514230
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:170499846..170504184-chr1:170513564..170517681,4	K562	blood:
2	chr1:170507810..170510159-chr1:170513671..170515970,2	MCF-7	breast:
3	chr1:170500119..170501652-chr1:170512143..170514479,2	MCF-7	breast:
4	chr1:170499494..170507345-chr1:170507805..170517333,18	K562	blood:

Variant related genes	Relation type
ENSG00000120370	Chromatin interaction
ENSG00000231407	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10800526	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10919391	1.00[ASN][1000 genomes]
rs10919403	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10919405	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10919406	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10919408	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10919410	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10919416	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10919417	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10919421	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10919423	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10919424	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10919426	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10919430	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1113231	0.82[ASW][hapmap];1.00[CHB][hapmap];0.83[GIH][hapmap];0.93[MKK][hapmap]
rs11577004	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11578119	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11584810	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11587811	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12066718	1.00[ASN][1000 genomes]
rs12116863	0.92[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12116910	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12120718	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12123065	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12124354	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12124515	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12126472	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12128140	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12128573	0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12130086	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12130520	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12132914	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12134482	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12135132	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];0.84[MEX][hapmap];1.00[MKK][hapmap];0.81[TSI][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12135326	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12137818	0.92[AFR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12138138	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12138428	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12139124	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12140689	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12141076	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12142689	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12145961	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12402306	0.89[ASN][1000 genomes]
rs12402526	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12405323	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12408130	0.83[AFR][1000 genomes]
rs12409985	0.82[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs12724601	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1333142	0.92[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1412890	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1537390	0.92[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1591150	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17350312	0.96[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs1888173	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1928716	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.81[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1999523	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];0.84[MEX][hapmap];1.00[MKK][hapmap];0.81[TSI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2183372	0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2421326	0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3923079	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4281371	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4399219	1.00[ASN][1000 genomes]
rs4508077	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4656776	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4656781	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6427253	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66639118	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6667728	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6675683	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6696114	0.83[EUR][1000 genomes]
rs6698352	0.82[ASW][hapmap];1.00[CHB][hapmap]
rs72709772	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72709774	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7511715	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7519067	0.82[AFR][1000 genomes];0.82[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	nsv872543	chr1:170171083-170674903	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv533915	chr1:170258766-170725296	Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12120764	RXRG	cis	parietal	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:170501800-170516000	Weak transcription	Spleen	Spleen
2	chr1:170502000-170515200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr1:170502000-170517200	Weak transcription	Esophagus	oesophagus
4	chr1:170502200-170521000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:170502400-170514800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr1:170502600-170520800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr1:170502600-170523400	Weak transcription	Fetal Brain Male	brain
8	chr1:170503000-170516400	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr1:170503000-170523600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr1:170503800-170516000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr1:170505000-170524800	Strong transcription	Dnd41	blood
12	chr1:170505400-170522800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr1:170506000-170522200	Strong transcription	Primary B cells from cord blood	blood
14	chr1:170506600-170516800	Strong transcription	HUES64 Cell Line	embryonic stem cell
15	chr1:170506600-170519200	Weak transcription	Gastric	stomach
16	chr1:170506600-170519200	Weak transcription	Right Ventricle	heart
17	chr1:170507400-170516400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr1:170507400-170516400	Weak transcription	HSMMtube	muscle
19	chr1:170507600-170515800	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr1:170507600-170516200	Weak transcription	Stomach Mucosa	stomach
21	chr1:170507600-170523600	Strong transcription	Primary B cells from peripheral blood	blood
22	chr1:170507600-170524000	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr1:170507800-170516400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr1:170507800-170521800	Strong transcription	Fetal Lung	lung
25	chr1:170507800-170522200	Strong transcription	Primary T cells fromperipheralblood	blood
26	chr1:170507800-170522600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
27	chr1:170508000-170514600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr1:170508000-170516400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr1:170508000-170522000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr1:170508000-170523000	Strong transcription	HUES48 Cell Line	embryonic stem cell
31	chr1:170508200-170516400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr1:170508200-170522200	Strong transcription	HUES6 Cell Line	embryonic stem cell
33	chr1:170508200-170523400	Strong transcription	Primary T helper cells fromperipheralblood	blood
34	chr1:170508200-170524400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr1:170508400-170515200	Strong transcription	Duodenum Smooth Muscle	Duodenum
36	chr1:170508400-170515200	Strong transcription	Skeletal Muscle Female	skeletal muscle
37	chr1:170508400-170516400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr1:170508400-170519600	Strong transcription	H1 Cell Line	embryonic stem cell
39	chr1:170508400-170521600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr1:170508400-170522000	Strong transcription	Placenta	Placenta
41	chr1:170508400-170522200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
42	chr1:170508400-170522200	Strong transcription	Primary hematopoietic stem cells	blood
43	chr1:170508400-170522200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr1:170508400-170522200	Strong transcription	Duodenum Mucosa	Duodenum
45	chr1:170508400-170522200	Strong transcription	Fetal Thymus	thymus
46	chr1:170508400-170522200	Strong transcription	Rectal Mucosa Donor 29	rectum
47	chr1:170508400-170522400	Strong transcription	Primary T helper cells PMA-I stimulated	--
48	chr1:170508400-170523600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr1:170508400-170523600	Strong transcription	Rectal Mucosa Donor 31	rectum
50	chr1:170508400-170523800	Strong transcription	Primary monocytes fromperipheralblood	blood

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