Variant report

Variant	rs6930131
Chromosome Location	chr6:79940778-79940779
allele	A/G
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	chr6:79940694-79942055	PBDE	blood:	n/a	chr6:79940857-79940878 chr6:79941496-79941503 chr6:79940862-79940872 chr6:79940698-79940708 chr6:79941493-79941503 chr6:79941584-79941600 chr6:79941495-79941505 chr6:79941492-79941508 chr6:79941496-79941505 chr6:79941494-79941506

No.	Distal block	Cell Line	Cell type
1	chr6:79786884..79788713-chr6:79939941..79941491,2	K562	blood:
2	chr6:79938105..79940918-chr6:79942151..79944715,2	K562	blood:
3	chr6:79782683..79789958-chr6:79939846..79945776,22	MCF-7	breast:
4	chr6:79786645..79789143-chr6:79938512..79942027,3	MCF-7	breast:

Variant related genes	Relation type
HMGN3-AS1	TF binding region
ENSG00000118418	Chromatin interaction
ENSG00000270362	Chromatin interaction
ENSG00000146247	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10806164	0.93[EUR][1000 genomes]
rs11752249	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs12191359	0.93[EUR][1000 genomes]
rs12191682	0.83[ASW][hapmap]
rs12211094	0.93[EUR][1000 genomes]
rs13209338	0.84[GIH][hapmap]
rs13213305	0.84[GIH][hapmap]
rs2050436	0.93[EUR][1000 genomes]
rs28360567	0.93[EUR][1000 genomes]
rs28360568	0.93[EUR][1000 genomes]
rs34043789	0.96[EUR][1000 genomes]
rs35711640	0.93[EUR][1000 genomes]
rs4706085	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4706757	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs66732383	0.93[EUR][1000 genomes]
rs7750289	0.93[EUR][1000 genomes]
rs7766859	0.93[EUR][1000 genomes]
rs9294132	1.00[CEU][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9294133	0.88[ASW][hapmap];0.91[CEU][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];0.82[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9294134	1.00[CEU][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9343882	0.93[EUR][1000 genomes]
rs9361502	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9448657	0.91[CEU][hapmap];0.84[GIH][hapmap];0.89[TSI][hapmap];0.96[EUR][1000 genomes]
rs989191	1.00[CEU][hapmap];0.84[GIH][hapmap];0.95[TSI][hapmap];0.99[EUR][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	nsv830706	chr6:79825910-79994878	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1028607	chr6:79853272-80767716	Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6930131	HMGN3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:79907400-79942800	Weak transcription	HSMM	muscle
2	chr6:79907600-79940800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr6:79912800-79942600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr6:79913200-79943000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr6:79913200-79943200	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr6:79916400-79943200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr6:79917800-79941000	Weak transcription	Hela-S3	cervix
8	chr6:79918200-79942000	Weak transcription	Primary T cells fromperipheralblood	blood
9	chr6:79920400-79943000	Weak transcription	Fetal Muscle Trunk	muscle
10	chr6:79925400-79942600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr6:79925800-79941800	Weak transcription	Brain Angular Gyrus	brain
12	chr6:79925800-79942000	Weak transcription	Adipose Nuclei	Adipose
13	chr6:79925800-79942000	Weak transcription	Brain Anterior Caudate	brain
14	chr6:79925800-79942800	Weak transcription	Liver	Liver
15	chr6:79926600-79942000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr6:79927400-79942600	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr6:79927600-79940800	Weak transcription	Brain Hippocampus Middle	brain
18	chr6:79927800-79940800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr6:79927800-79942000	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr6:79927800-79942800	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr6:79927800-79942800	Weak transcription	Primary T cells from cord blood	blood
22	chr6:79928000-79942000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr6:79929000-79942000	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr6:79929000-79942000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr6:79929200-79941600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr6:79929600-79941400	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr6:79929800-79941000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr6:79930200-79941800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr6:79931200-79942800	Weak transcription	Left Ventricle	heart
30	chr6:79931600-79942000	Weak transcription	Gastric	stomach
31	chr6:79932400-79942400	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr6:79933800-79942600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr6:79934200-79942200	Weak transcription	Primary hematopoietic stem cells	blood
34	chr6:79934200-79942400	Weak transcription	Primary B cells from cord blood	blood
35	chr6:79934600-79941600	Weak transcription	Fetal Intestine Small	intestine
36	chr6:79935800-79941600	Weak transcription	Colon Smooth Muscle	Colon
37	chr6:79935800-79942000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr6:79936000-79942000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr6:79936200-79940800	Weak transcription	Right Ventricle	heart
40	chr6:79936200-79941400	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr6:79936200-79941600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr6:79936200-79942200	Weak transcription	Small Intestine	intestine
43	chr6:79936200-79943000	Weak transcription	Fetal Intestine Large	intestine
44	chr6:79936200-79943000	Weak transcription	Psoas Muscle	Psoas
45	chr6:79936200-79943200	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr6:79936800-79941000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr6:79936800-79941000	Weak transcription	Fetal Heart	heart
48	chr6:79936800-79941600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr6:79936800-79942800	Weak transcription	Fetal Kidney	kidney
50	chr6:79937400-79942600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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