Variant report

Variant	rs2079431
Chromosome Location	chr22:31564334-31564335
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:31555610..31558021-chr22:31563068..31564682,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000138942	Chromatin interaction
ENSG00000264141	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs1034588	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1034589	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13056485	0.91[CHB][hapmap];0.88[JPT][hapmap]
rs13158	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1858821	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs2040533	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs2073857	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2078803	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs2106294	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2228619	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2232170	0.85[CEU][hapmap]
rs2232176	0.85[CEU][hapmap]
rs2283879	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2283881	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2413031	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2413032	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2413033	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2413034	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2413035	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2413046	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2413047	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2413049	0.85[EUR][1000 genomes]
rs4141404	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs4299418	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4603880	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs4820042	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4820043	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs4820951	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4820955	1.00[CEU][hapmap]
rs4820962	0.81[EUR][1000 genomes]
rs4820963	1.00[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs5749224	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5749229	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs5753500	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5753505	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs5753507	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs5753521	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs5753543	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs5997902	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5997912	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs5997913	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs5997933	0.85[EUR][1000 genomes]
rs5997939	0.89[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs714909	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs715510	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs7287267	0.81[EUR][1000 genomes]
rs737684	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs737887	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs737888	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8135344	0.89[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs8135347	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9606830	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]
rs9606831	0.81[EUR][1000 genomes]
rs9609264	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs9609265	0.81[EUR][1000 genomes]
rs9609266	0.81[EUR][1000 genomes]
rs9609267	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv459871	chr22:31551160-31680624	Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
2	nsv588893	chr22:31551160-31680624	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
3	nsv1067003	chr22:31558663-31697093	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2079431	DRG1	Cis_1M	lymphoblastoid	RTeQTL
rs2079431	SFI1	cis	Thyroid	GTEx

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:31557000-31569400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr22:31557000-31573000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr22:31557000-31575200	Weak transcription	Esophagus	oesophagus
4	chr22:31557200-31568800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr22:31557200-31569400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr22:31557200-31591200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr22:31557400-31565800	Weak transcription	Spleen	Spleen
8	chr22:31557400-31569200	Weak transcription	A549	lung
9	chr22:31557400-31575000	Weak transcription	Gastric	stomach
10	chr22:31557400-31579800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr22:31557400-31595200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr22:31557400-31597800	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr22:31557600-31564600	Weak transcription	Right Ventricle	heart
14	chr22:31557600-31575000	Weak transcription	Colonic Mucosa	Colon
15	chr22:31557600-31578600	Weak transcription	K562	blood
16	chr22:31557600-31591800	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr22:31557800-31568800	Weak transcription	Hela-S3	cervix
18	chr22:31557800-31569400	Weak transcription	Ovary	ovary
19	chr22:31557800-31587000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr22:31557800-31588400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr22:31558000-31578000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr22:31558200-31565000	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr22:31558200-31573000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr22:31558200-31575000	Weak transcription	Stomach Mucosa	stomach
25	chr22:31558400-31568800	Weak transcription	HMEC	breast
26	chr22:31558400-31569200	Weak transcription	Rectal Smooth Muscle	rectum
27	chr22:31558400-31573000	Weak transcription	Fetal Heart	heart
28	chr22:31558600-31565800	Weak transcription	Primary neutrophils fromperipheralblood	blood
29	chr22:31558600-31583000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr22:31558600-31591400	Weak transcription	Primary hematopoietic stem cells	blood
31	chr22:31558800-31564600	Weak transcription	Aorta	Aorta
32	chr22:31558800-31568800	Weak transcription	Small Intestine	intestine
33	chr22:31558800-31572800	Weak transcription	Brain Germinal Matrix	brain
34	chr22:31558800-31591200	Weak transcription	Fetal Brain Male	brain
35	chr22:31558800-31606000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr22:31559200-31564800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr22:31559200-31564800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr22:31559200-31567000	Strong transcription	Fetal Intestine Small	intestine
39	chr22:31559200-31567000	Strong transcription	Fetal Stomach	stomach
40	chr22:31559400-31565000	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr22:31559600-31564400	Strong transcription	Fetal Muscle Trunk	muscle
42	chr22:31559600-31568400	Weak transcription	NHLF	lung
43	chr22:31559600-31572800	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr22:31559600-31575000	Weak transcription	Pancreas	Pancrea
45	chr22:31560400-31564400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
46	chr22:31560400-31564800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr22:31560800-31569200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr22:31561000-31564600	Strong transcription	Rectal Mucosa Donor 29	rectum
49	chr22:31561000-31564600	Strong transcription	Dnd41	blood
50	chr22:31561200-31564400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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