Variant report

Variant	rs59310759
Chromosome Location	chr6:34320035-34320036
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:34318109..34321086-chr6:34360029..34361626,2	MCF-7	breast:
2	chr6:34311894..34313491-chr6:34319028..34320786,2	K562	blood:
3	chr6:34314465..34317126-chr6:34317621..34320996,4	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HMGA1-7	chr6:34319922-34320322	expReg_chr6_3789_+

Variant related genes	Relation type
ENSG00000272325	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs12662460	0.86[ASN][1000 genomes]
rs12664001	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12665397	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16885998	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16889706	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16889714	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2071928	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34384951	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3778077	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3798562	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3798564	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3800476	0.81[AMR][1000 genomes]
rs3800477	0.81[AMR][1000 genomes]
rs4711390	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4713770	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4713772	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4713773	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4713774	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4713775	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4713776	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4713777	0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4713780	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4713781	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4713783	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4713784	0.81[AMR][1000 genomes]
rs4713787	0.84[AMR][1000 genomes]
rs58648597	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60100381	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62399909	0.86[ASN][1000 genomes]
rs6924682	0.89[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6935129	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7752035	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7767431	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9766229	0.82[AMR][1000 genomes]

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	esv3509192	chr6:34315574-34320922	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	esv3509193	chr6:34315574-34320922	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	esv3526073	chr6:34315874-34320672	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	esv1799298	chr6:34317120-34322841	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv1022844	chr6:34317219-35060519	Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
6	nsv538195	chr6:34317219-35060519	Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:34261800-34330800	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr6:34285200-34330600	Weak transcription	Thymus	Thymus
3	chr6:34285800-34326600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr6:34289000-34325200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr6:34298600-34326400	Weak transcription	A549	lung
6	chr6:34306000-34327800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr6:34306000-34328800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr6:34308800-34330800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr6:34309600-34329200	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr6:34309800-34320200	Weak transcription	HepG2	liver
11	chr6:34309800-34321400	Weak transcription	Lung	lung
12	chr6:34309800-34327000	Weak transcription	Fetal Muscle Trunk	muscle
13	chr6:34309800-34329800	Weak transcription	Fetal Thymus	thymus
14	chr6:34309800-34330800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr6:34309800-34337600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr6:34309800-34347200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr6:34310000-34320200	Weak transcription	Fetal Stomach	stomach
18	chr6:34310000-34330600	Weak transcription	Dnd41	blood
19	chr6:34310400-34321600	Weak transcription	Right Ventricle	heart
20	chr6:34310400-34329200	Weak transcription	Brain Angular Gyrus	brain
21	chr6:34310600-34326400	Weak transcription	Rectal Smooth Muscle	rectum
22	chr6:34310800-34330800	Weak transcription	Primary T cells from cord blood	blood
23	chr6:34311200-34321800	Weak transcription	Psoas Muscle	Psoas
24	chr6:34314800-34320200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr6:34315400-34351200	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr6:34316200-34333400	Weak transcription	Placenta	Placenta
27	chr6:34317000-34320400	Enhancers	Primary monocytes fromperipheralblood	blood
28	chr6:34317400-34330800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr6:34318000-34320200	Enhancers	Primary B cells from cord blood	blood
30	chr6:34318000-34320400	Enhancers	K562	blood
31	chr6:34318200-34326400	Weak transcription	Fetal Muscle Leg	muscle
32	chr6:34318200-34330600	Weak transcription	Brain Hippocampus Middle	brain
33	chr6:34318200-34355800	Weak transcription	Brain Germinal Matrix	brain
34	chr6:34318400-34326000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr6:34318400-34330000	Weak transcription	Primary hematopoietic stem cells	blood
36	chr6:34318600-34330600	Weak transcription	Fetal Intestine Small	intestine
37	chr6:34318800-34320200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr6:34318800-34320200	Weak transcription	Brain Anterior Caudate	brain
39	chr6:34318800-34320200	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr6:34318800-34320600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr6:34318800-34323600	Weak transcription	Brain Substantia Nigra	brain
42	chr6:34318800-34325600	Weak transcription	Fetal Heart	heart
43	chr6:34318800-34325800	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr6:34318800-34327400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr6:34318800-34330600	Weak transcription	Adipose Nuclei	Adipose
46	chr6:34319000-34320200	Weak transcription	Liver	Liver
47	chr6:34319000-34320400	Enhancers	Left Ventricle	heart
48	chr6:34319400-34320200	Enhancers	Sigmoid Colon	Sigmoid Colon
49	chr6:34319400-34327600	Weak transcription	Right Atrium	heart
50	chr6:34319800-34320400	Enhancers	Primary neutrophils fromperipheralblood	blood

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