Variant report

Variant	rs10512930
Chromosome Location	chr5:7906576-7906577
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10066017	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10475399	0.89[JPT][hapmap]
rs10520873	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12186809	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13166314	0.89[JPT][hapmap]
rs16879418	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16879420	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17267793	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3776455	0.89[JPT][hapmap]
rs3776457	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3776465	0.95[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3797191	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3822441	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55872008	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56149723	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57240487	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57989551	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59253244	0.83[EUR][1000 genomes]
rs62342528	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62342552	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62342558	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62345660	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs67514505	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs67902045	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7703033	0.95[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8659	0.85[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916892	chr5:7634377-8158890	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv949492	chr5:7682909-7953909	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv533983	chr5:7701457-8275379	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv597005	chr5:7860404-8093077	Enhancers Strong transcription Genic enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv427707	chr5:7866234-7966019	Strong transcription Active TSS Genic enhancers Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
6	nsv508345	chr5:7890892-7933471	Strong transcription Weak transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10512930	MTRR	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:7871600-7906800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr5:7871800-7907400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
3	chr5:7874000-7909200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr5:7875000-7906600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr5:7878600-7911800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr5:7880400-7906600	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr5:7880600-7907000	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr5:7887600-7906800	Strong transcription	Primary T helper cells PMA-I stimulated	--
9	chr5:7888600-7906600	Strong transcription	Primary T helper cells fromperipheralblood	blood
10	chr5:7895400-7909600	Weak transcription	Fetal Heart	heart
11	chr5:7899600-7910000	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr5:7899600-7912000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr5:7899800-7909200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr5:7899800-7909200	Weak transcription	Esophagus	oesophagus
15	chr5:7900000-7909600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr5:7900000-7914600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr5:7900600-7907000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr5:7900600-7909200	Weak transcription	Gastric	stomach
19	chr5:7902200-7909000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr5:7902400-7907800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr5:7902400-7907800	Weak transcription	Psoas Muscle	Psoas
22	chr5:7902400-7909000	Weak transcription	Aorta	Aorta
23	chr5:7902400-7909000	Weak transcription	Right Ventricle	heart
24	chr5:7902400-7909000	Weak transcription	K562	blood
25	chr5:7902400-7910200	Weak transcription	Fetal Brain Male	brain
26	chr5:7902400-7910800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr5:7902400-7911200	Weak transcription	Fetal Kidney	kidney
28	chr5:7902800-7907600	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr5:7902800-7911200	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr5:7903000-7907000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr5:7903000-7907200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr5:7903200-7907000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr5:7903400-7907000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr5:7903400-7907200	Weak transcription	Dnd41	blood
35	chr5:7903400-7907400	Weak transcription	Brain Substantia Nigra	brain
36	chr5:7903400-7908200	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr5:7903400-7908200	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr5:7903400-7909000	Weak transcription	Colonic Mucosa	Colon
39	chr5:7903400-7909200	Weak transcription	Rectal Smooth Muscle	rectum
40	chr5:7903400-7911000	Weak transcription	Fetal Thymus	thymus
41	chr5:7903600-7907000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr5:7903600-7907200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr5:7903600-7908200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr5:7903600-7909000	Weak transcription	Brain Angular Gyrus	brain
45	chr5:7903600-7909200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr5:7903600-7916000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr5:7903800-7907000	Weak transcription	HUES6 Cell Line	embryonic stem cell
48	chr5:7903800-7907600	Weak transcription	GM12878-XiMat	blood
49	chr5:7903800-7907800	Weak transcription	Primary B cells from peripheral blood	blood
50	chr5:7903800-7913600	Weak transcription	Skeletal Muscle Male	skeletal muscle

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