Variant report

Variant	rs6794484
Chromosome Location	chr3:119390219-119390220
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:119388635..119391771-chr3:119394131..119397043,3	MCF-7	breast:
2	chr3:119328437..119330333-chr3:119390205..119392685,2	K562	blood:
3	chr3:119377372..119379623-chr3:119387851..119390487,2	K562	blood:
4	chr3:119388646..119390230-chr3:119392331..119393863,2	K562	blood:
5	chr3:119389108..119393521-chr3:119393632..119397776,6	MCF-7	breast:
6	chr3:119389471..119391263-chr3:119394151..119396440,3	K562	blood:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-POPDC2-3	chr3:119389611-119390692	NONHSAT091402

No data

Variant related genes	Relation type
ENSG00000138495	Chromatin interaction
ENSG00000121577	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11720605	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13062540	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1317259	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1880041	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2046430	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2629397	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2629409	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2670296	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2688633	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2692618	0.88[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2698282	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3772134	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4327424	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs523476	1.00[CEU][hapmap];0.87[YRI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs552244	1.00[CEU][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs571352	1.00[CEU][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62265884	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6438541	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6438542	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6782253	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6785698	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6794579	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6797667	0.95[YRI][hapmap]
rs6807079	1.00[CEU][hapmap];0.81[YRI][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs693397	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7613999	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7633444	1.00[CEU][hapmap];0.88[YRI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs940181	0.83[AMR][1000 genomes];0.91[EUR][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	esv3487859	chr3:118570588-119419623	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer 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	61 gene(s)	inside rSNPs	diseases
2	esv3487860	chr3:118570588-119419623	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	esv1831824	chr3:119263607-119402474	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv1014394	chr3:119360506-119412275	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv460834	chr3:119384163-119458851	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	nsv591390	chr3:119384163-119458851	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6794484	POPDC2	cis	Thyroid	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119356800-119391800	Weak transcription	Brain Substantia Nigra	brain
2	chr3:119356800-119391800	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr3:119358000-119390600	Weak transcription	Brain Anterior Caudate	brain
4	chr3:119358000-119391800	Weak transcription	Colonic Mucosa	Colon
5	chr3:119361200-119394400	Weak transcription	Brain Angular Gyrus	brain
6	chr3:119367600-119391200	Weak transcription	Fetal Brain Female	brain
7	chr3:119379200-119391800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr3:119379200-119392400	Weak transcription	Esophagus	oesophagus
9	chr3:119379200-119392400	Weak transcription	Gastric	stomach
10	chr3:119379800-119391800	Weak transcription	Thymus	Thymus
11	chr3:119380000-119391800	Weak transcription	Lung	lung
12	chr3:119380000-119391800	Weak transcription	Ovary	ovary
13	chr3:119380000-119391800	Weak transcription	Pancreas	Pancrea
14	chr3:119380000-119391800	Weak transcription	Spleen	Spleen
15	chr3:119380000-119392000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr3:119380400-119391000	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr3:119381000-119392000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr3:119382200-119390600	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr3:119382400-119390600	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr3:119382400-119391000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr3:119382400-119391800	Weak transcription	Fetal Stomach	stomach
22	chr3:119382600-119391800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr3:119383800-119390600	Weak transcription	Brain Germinal Matrix	brain
24	chr3:119383800-119393800	Strong transcription	Primary B cells from cord blood	blood
25	chr3:119384000-119391800	Weak transcription	HSMMtube	muscle
26	chr3:119384000-119395000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr3:119384200-119391600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr3:119384200-119394400	Weak transcription	Stomach Mucosa	stomach
29	chr3:119384400-119391000	Weak transcription	Fetal Intestine Small	intestine
30	chr3:119384400-119391200	Weak transcription	Fetal Kidney	kidney
31	chr3:119384400-119391200	Weak transcription	Stomach Smooth Muscle	stomach
32	chr3:119384600-119391600	Weak transcription	K562	blood
33	chr3:119384600-119391800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr3:119384600-119392400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr3:119384600-119394600	Weak transcription	NH-A	brain
36	chr3:119385200-119392200	Weak transcription	Osteobl	bone
37	chr3:119385400-119394200	Strong transcription	Primary T cells from cord blood	blood
38	chr3:119385400-119394400	Strong transcription	Primary T helper cells PMA-I stimulated	--
39	chr3:119385600-119394200	Strong transcription	Primary monocytes fromperipheralblood	blood
40	chr3:119385600-119394200	Strong transcription	Primary neutrophils fromperipheralblood	blood
41	chr3:119385600-119394200	Strong transcription	Fetal Thymus	thymus
42	chr3:119385600-119394400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr3:119385600-119394600	Strong transcription	Monocytes-CD14+_RO01746	blood
44	chr3:119385800-119390600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr3:119385800-119391200	Strong transcription	Duodenum Smooth Muscle	Duodenum
46	chr3:119385800-119394000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
47	chr3:119385800-119394000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
48	chr3:119385800-119394000	Strong transcription	Rectal Mucosa Donor 29	rectum
49	chr3:119386000-119390600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr3:119386000-119394200	Strong transcription	Primary T helper cells fromperipheralblood	blood

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