Variant report

Variant	rs10930497
Chromosome Location	chr2:172733842-172733843
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:172733666..172736692-chr2:172737293..172740256,4	K562	blood:
2	chr2:172733649..172740490-chr2:172749209..172752081,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115840	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10177679	1.00[CEU][hapmap]
rs10185633	1.00[CEU][hapmap]
rs10196521	1.00[CEU][hapmap]
rs11676484	1.00[CEU][hapmap]
rs12471160	1.00[AFR][1000 genomes]
rs12473516	1.00[MEX][hapmap]
rs12473876	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12479374	1.00[CEU][hapmap]
rs1400816	1.00[CEU][hapmap]
rs1543168	1.00[CEU][hapmap]
rs1607253	1.00[CEU][hapmap]
rs16859721	1.00[CEU][hapmap]
rs17580984	1.00[CEU][hapmap]
rs17581715	1.00[CEU][hapmap]
rs17614989	1.00[CEU][hapmap]
rs17615013	1.00[CEU][hapmap]
rs1878583	1.00[CEU][hapmap]
rs1982288	1.00[CEU][hapmap]
rs2028670	1.00[CEU][hapmap]
rs2028671	1.00[CEU][hapmap]
rs2028672	1.00[CEU][hapmap]
rs2037164	1.00[CEU][hapmap]
rs2292813	1.00[CEU][hapmap]
rs2292814	1.00[CEU][hapmap]
rs2357208	1.00[CEU][hapmap]
rs28372952	1.00[CEU][hapmap]
rs312917	1.00[CEU][hapmap]
rs3770443	1.00[CEU][hapmap]
rs3770457	1.00[CEU][hapmap]
rs3791343	1.00[AFR][1000 genomes]
rs3821092	1.00[CEU][hapmap]
rs3821094	1.00[CEU][hapmap]
rs3821096	1.00[CEU][hapmap]
rs4668417	1.00[CEU][hapmap]
rs6433313	1.00[CEU][hapmap]
rs6433315	1.00[CEU][hapmap]
rs6433318	1.00[CEU][hapmap]
rs6433322	1.00[CEU][hapmap]
rs6707142	1.00[CEU][hapmap]
rs6714214	1.00[CEU][hapmap]
rs6753859	1.00[CEU][hapmap]
rs718936	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7560031	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7579509	0.82[CEU][hapmap]
rs7580132	0.82[CEU][hapmap]
rs7607377	1.00[ASN][1000 genomes]
rs9287948	1.00[CEU][hapmap]
rs949548	1.00[CEU][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	nsv834457	chr2:172564939-172770901	Strong transcription Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS 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 target site	14 gene(s)	inside rSNPs	diseases
2	nsv583611	chr2:172683481-172750257	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
3	nsv1006214	chr2:172691689-172754296	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
4	nsv536036	chr2:172691689-172754296	Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
5	nsv875410	chr2:172693780-172896587	Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
6	nsv875411	chr2:172693780-172942448	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10930497	FGD5	trans	lymphoblastoid	seeQTL

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:172690200-172750200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr2:172691400-172738600	Weak transcription	Esophagus	oesophagus
3	chr2:172693400-172734800	Weak transcription	Brain Hippocampus Middle	brain
4	chr2:172693600-172734400	Weak transcription	Rectal Smooth Muscle	rectum
5	chr2:172693600-172734600	Weak transcription	HSMM	muscle
6	chr2:172693800-172734600	Weak transcription	Right Ventricle	heart
7	chr2:172694000-172734600	Weak transcription	Brain Cingulate Gyrus	brain
8	chr2:172694000-172734600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr2:172698600-172734600	Weak transcription	Adipose Nuclei	Adipose
10	chr2:172699000-172734600	Weak transcription	Brain Angular Gyrus	brain
11	chr2:172705400-172735200	Weak transcription	Stomach Smooth Muscle	stomach
12	chr2:172709400-172734400	Weak transcription	Colon Smooth Muscle	Colon
13	chr2:172709600-172749600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr2:172709600-172749600	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr2:172710800-172747800	Weak transcription	Primary T helper cells fromperipheralblood	blood
16	chr2:172711600-172740000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr2:172712200-172749200	Weak transcription	Hela-S3	cervix
18	chr2:172712400-172738200	Weak transcription	Primary hematopoietic stem cells	blood
19	chr2:172715400-172735200	Weak transcription	NHLF	lung
20	chr2:172716600-172736600	Weak transcription	Ovary	ovary
21	chr2:172721200-172734600	Weak transcription	Right Atrium	heart
22	chr2:172721200-172734600	Weak transcription	HSMMtube	muscle
23	chr2:172721200-172749600	Weak transcription	Thymus	Thymus
24	chr2:172721400-172734600	Weak transcription	Aorta	Aorta
25	chr2:172721400-172734600	Weak transcription	Brain Anterior Caudate	brain
26	chr2:172721400-172734600	Weak transcription	Psoas Muscle	Psoas
27	chr2:172724000-172749600	Weak transcription	Small Intestine	intestine
28	chr2:172724800-172749600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr2:172725200-172734600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr2:172725200-172735000	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr2:172725400-172749800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr2:172725800-172734400	Weak transcription	K562	blood
33	chr2:172725800-172749600	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr2:172727800-172738600	Weak transcription	Dnd41	blood
35	chr2:172728200-172734600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr2:172731200-172734600	Weak transcription	Stomach Mucosa	stomach
37	chr2:172731400-172746400	Weak transcription	Fetal Lung	lung
38	chr2:172731600-172749600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr2:172731800-172734600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr2:172731800-172734800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr2:172731800-172735000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr2:172731800-172735200	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr2:172731800-172740600	Weak transcription	Fetal Stomach	stomach
44	chr2:172731800-172746400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr2:172732000-172734400	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr2:172732000-172734600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr2:172732000-172734600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
48	chr2:172732000-172734800	Weak transcription	Brain Germinal Matrix	brain
49	chr2:172732000-172735200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr2:172732000-172736000	Weak transcription	Cortex derived primary cultured neurospheres	brain

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