Variant report

Variant	rs2279561
Chromosome Location	chr3:158431702-158431703
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA1	chr3:158430593-158431762	PBDE	blood:	n/a	chr3:158431260-158431269 chr3:158431230-158431240

No.	Distal block	Cell Line	Cell type
1	chr3:158431692..158434686-chr3:158440756..158442982,2	K562	blood:
2	chr3:158430342..158432825-chr3:158434955..158438595,5	K562	blood:
3	chr3:158423211..158426282-chr3:158428433..158432187,3	K562	blood:
4	chr3:158429563..158432825-chr3:158433996..158437681,6	K562	blood:

Variant related genes	Relation type
RARRES1	TF binding region
ENSG00000118849	Chromatin interaction

Extended variants
information (count: 100 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs10513528	0.87[YRI][hapmap]
rs12489730	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12491877	0.94[ASN][1000 genomes]
rs12495962	0.81[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs12497488	0.95[ASN][1000 genomes]
rs1430413	0.95[ASN][1000 genomes]
rs1430414	0.95[ASN][1000 genomes]
rs1560417	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.95[ASN][1000 genomes]
rs1560418	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.95[ASN][1000 genomes]
rs16829365	0.89[ASN][1000 genomes]
rs17630607	0.90[CEU][hapmap];0.82[AMR][1000 genomes]
rs17630980	0.82[JPT][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17642769	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17643171	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17643252	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17643483	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17643581	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17643860	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs17643917	0.92[JPT][hapmap];0.88[ASN][1000 genomes]
rs17697458	0.90[CEU][hapmap];0.82[AMR][1000 genomes]
rs17698494	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17699103	0.90[CEU][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17699324	0.90[CEU][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17699478	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17699526	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17699997	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17700122	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17700475	0.95[ASN][1000 genomes]
rs2279562	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2304408	0.90[CEU][hapmap]
rs2307064	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2566347	0.95[ASN][1000 genomes]
rs28372852	0.82[AMR][1000 genomes]
rs34690420	0.95[ASN][1000 genomes]
rs3863076	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs3867391	0.90[CEU][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs41434057	0.86[YRI][hapmap]
rs55666734	0.82[AMR][1000 genomes]
rs55678388	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55705231	0.94[ASN][1000 genomes]
rs55717824	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55776609	0.88[ASN][1000 genomes]
rs56023805	0.95[ASN][1000 genomes]
rs56075263	0.80[AMR][1000 genomes]
rs56078503	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56089835	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs56105525	0.95[ASN][1000 genomes]
rs56152025	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56167308	0.82[AMR][1000 genomes]
rs56235582	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56261306	0.95[ASN][1000 genomes]
rs56318834	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57262841	0.95[ASN][1000 genomes]
rs59163359	0.95[ASN][1000 genomes]
rs59173444	0.89[ASN][1000 genomes]
rs60203196	0.81[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs60942689	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs61138408	0.95[ASN][1000 genomes]
rs61794798	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61794799	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61794818	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61794821	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61794822	0.95[ASN][1000 genomes]
rs61794833	0.95[ASN][1000 genomes]
rs61794834	0.95[ASN][1000 genomes]
rs61794835	0.91[ASN][1000 genomes]
rs61794858	0.95[ASN][1000 genomes]
rs61794859	0.95[ASN][1000 genomes]
rs61796762	0.95[ASN][1000 genomes]
rs61796764	0.94[ASN][1000 genomes]
rs61796768	0.94[ASN][1000 genomes]
rs61796770	0.94[ASN][1000 genomes]
rs62286650	0.82[AMR][1000 genomes]
rs62286654	0.82[AMR][1000 genomes]
rs62288303	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs62288305	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62288306	0.82[AMR][1000 genomes]
rs62288307	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62288344	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62288345	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6441221	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6761989	0.95[ASN][1000 genomes]
rs6776901	0.90[CEU][hapmap];0.82[AMR][1000 genomes]
rs6777231	0.90[CEU][hapmap];0.82[AMR][1000 genomes]
rs6783610	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6792908	0.95[ASN][1000 genomes]
rs73158361	0.94[ASN][1000 genomes]
rs7610009	0.90[CEU][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7624420	0.92[JPT][hapmap];0.87[ASN][1000 genomes]
rs7624702	0.87[ASN][1000 genomes]
rs7628497	0.82[AMR][1000 genomes]
rs7633713	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002378	chr3:157715428-158673414	Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv1004124	chr3:158146715-158808638	Genic enhancers Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv530059	chr3:158332590-159147549	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv1014255	chr3:158358860-158768542	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv532665	chr3:158370013-158754245	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
6	nsv948755	chr3:158388780-158672287	Enhancers Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
7	nsv1007141	chr3:158415840-158433128	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	n/a
8	nsv877692	chr3:158430706-158828643	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2279561	GFM1	cis	Artery Tibial	GTEx
rs2279561	GFM1	cis	Esophagus Mucosa	GTEx
rs2279561	GFM1	cis	Muscle Skeletal	GTEx
rs2279561	GFM1	cis	Nerve Tibial	GTEx
rs2279561	LXN	Cis_1M	lymphoblastoid	RTeQTL
rs2279561	LXN	cis	multi-tissue	Pritchard
rs2279561	GFM1	cis	Thyroid	GTEx
rs2279561	GFM1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:158390800-158432800	Weak transcription	Spleen	Spleen
2	chr3:158390800-158444200	Weak transcription	Gastric	stomach
3	chr3:158390800-158445400	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr3:158391000-158438800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr3:158397000-158443400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr3:158397000-158448000	Weak transcription	Thymus	Thymus
7	chr3:158399600-158445400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr3:158403600-158438600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr3:158408400-158443000	Weak transcription	HepG2	liver
10	chr3:158409800-158439000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr3:158411600-158439400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr3:158412200-158440800	Weak transcription	Rectal Smooth Muscle	rectum
13	chr3:158412400-158439200	Weak transcription	Fetal Kidney	kidney
14	chr3:158415000-158440800	Weak transcription	Colonic Mucosa	Colon
15	chr3:158417600-158440600	Weak transcription	Aorta	Aorta
16	chr3:158421800-158435600	Strong transcription	Fetal Intestine Small	intestine
17	chr3:158423200-158431800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr3:158423800-158438800	Weak transcription	Primary T helper cells PMA-I stimulated	--
19	chr3:158424200-158446000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr3:158426400-158432400	Strong transcription	Fetal Intestine Large	intestine
21	chr3:158426400-158435200	Weak transcription	Fetal Brain Male	brain
22	chr3:158426600-158432400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr3:158426600-158436600	Strong transcription	Fetal Stomach	stomach
24	chr3:158426800-158432000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr3:158426800-158432200	Enhancers	NHLF	lung
26	chr3:158427200-158432000	Strong transcription	Fetal Muscle Leg	muscle
27	chr3:158427200-158435600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr3:158427600-158431800	Weak transcription	Lung	lung
29	chr3:158427600-158439000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr3:158427600-158440600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr3:158427800-158440400	Weak transcription	Primary monocytes fromperipheralblood	blood
32	chr3:158427800-158440600	Weak transcription	Duodenum Mucosa	Duodenum
33	chr3:158427800-158440800	Weak transcription	Liver	Liver
34	chr3:158427800-158440800	Weak transcription	Esophagus	oesophagus
35	chr3:158428000-158432200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr3:158428000-158434800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr3:158428000-158438800	Weak transcription	Fetal Brain Female	brain
38	chr3:158428600-158438800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
39	chr3:158429000-158440600	Weak transcription	Primary B cells from peripheral blood	blood
40	chr3:158429200-158432000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr3:158429200-158433600	Weak transcription	Placenta	Placenta
42	chr3:158429200-158438200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr3:158429400-158431800	Enhancers	HUVEC	blood vessel
44	chr3:158429400-158432000	Weak transcription	Fetal Muscle Trunk	muscle
45	chr3:158429400-158432400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr3:158429400-158436200	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr3:158429400-158438200	Weak transcription	Primary T helper cells fromperipheralblood	blood
48	chr3:158429600-158432200	Enhancers	NH-A	brain
49	chr3:158429600-158449000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr3:158429800-158432200	Enhancers	HUES6 Cell Line	embryonic stem cell

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