Variant report

Variant	rs7613999
Chromosome Location	chr3:119389745-119389746
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:7)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:119388635..119391771-chr3:119394131..119397043,3	MCF-7	breast:
2	chr3:119375861..119378454-chr3:119387094..119389806,2	K562	blood:
3	chr3:119377372..119379623-chr3:119387851..119390487,2	K562	blood:
4	chr3:119388646..119390230-chr3:119392331..119393863,2	K562	blood:
5	chr3:119383319..119384856-chr3:119387419..119389947,2	K562	blood:
6	chr3:119389108..119393521-chr3:119393632..119397776,6	MCF-7	breast:
7	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
ENSG00000121577	Chromatin interaction
ENSG00000138495	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs11720605	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13062540	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13065543	0.81[ASN][1000 genomes]
rs13065893	0.93[ASN][1000 genomes]
rs1317259	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1880040	0.91[ASN][1000 genomes]
rs1880041	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2046430	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2629395	0.92[ASN][1000 genomes]
rs2629397	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2629409	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2670296	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2688633	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2692618	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2698282	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3749416	0.93[ASN][1000 genomes]
rs3749417	0.93[ASN][1000 genomes]
rs3772134	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4327424	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4687871	0.90[ASN][1000 genomes]
rs4688023	0.91[ASN][1000 genomes]
rs484809	0.90[ASN][1000 genomes]
rs523476	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs552244	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs571352	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62265884	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6438541	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6438542	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6782253	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6785698	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6794484	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6794579	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6807079	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs693397	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7633444	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8007	0.90[ASN][1000 genomes]
rs940181	0.84[AMR][1000 genomes];0.92[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
rs7613999	POPDC2	cis	Thyroid	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119356800-119390000	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr3:119356800-119391800	Weak transcription	Brain Substantia Nigra	brain
3	chr3:119356800-119391800	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr3:119358000-119390600	Weak transcription	Brain Anterior Caudate	brain
5	chr3:119358000-119391800	Weak transcription	Colonic Mucosa	Colon
6	chr3:119361200-119394400	Weak transcription	Brain Angular Gyrus	brain
7	chr3:119363200-119389800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr3:119367600-119391200	Weak transcription	Fetal Brain Female	brain
9	chr3:119379200-119391800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr3:119379200-119392400	Weak transcription	Esophagus	oesophagus
11	chr3:119379200-119392400	Weak transcription	Gastric	stomach
12	chr3:119379800-119391800	Weak transcription	Thymus	Thymus
13	chr3:119380000-119391800	Weak transcription	Lung	lung
14	chr3:119380000-119391800	Weak transcription	Ovary	ovary
15	chr3:119380000-119391800	Weak transcription	Pancreas	Pancrea
16	chr3:119380000-119391800	Weak transcription	Spleen	Spleen
17	chr3:119380000-119392000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr3:119380400-119391000	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr3:119381000-119392000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr3:119382200-119390600	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr3:119382400-119390000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr3:119382400-119390600	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr3:119382400-119391000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr3:119382400-119391800	Weak transcription	Fetal Stomach	stomach
25	chr3:119382600-119391800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr3:119383800-119390600	Weak transcription	Brain Germinal Matrix	brain
27	chr3:119383800-119393800	Strong transcription	Primary B cells from cord blood	blood
28	chr3:119384000-119391800	Weak transcription	HSMMtube	muscle
29	chr3:119384000-119395000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr3:119384200-119391600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr3:119384200-119394400	Weak transcription	Stomach Mucosa	stomach
32	chr3:119384400-119391000	Weak transcription	Fetal Intestine Small	intestine
33	chr3:119384400-119391200	Weak transcription	Fetal Kidney	kidney
34	chr3:119384400-119391200	Weak transcription	Stomach Smooth Muscle	stomach
35	chr3:119384600-119391600	Weak transcription	K562	blood
36	chr3:119384600-119391800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr3:119384600-119392400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr3:119384600-119394600	Weak transcription	NH-A	brain
39	chr3:119385200-119389800	Weak transcription	Colon Smooth Muscle	Colon
40	chr3:119385200-119392200	Weak transcription	Osteobl	bone
41	chr3:119385400-119394200	Strong transcription	Primary T cells from cord blood	blood
42	chr3:119385400-119394400	Strong transcription	Primary T helper cells PMA-I stimulated	--
43	chr3:119385600-119394200	Strong transcription	Primary monocytes fromperipheralblood	blood
44	chr3:119385600-119394200	Strong transcription	Primary neutrophils fromperipheralblood	blood
45	chr3:119385600-119394200	Strong transcription	Fetal Thymus	thymus
46	chr3:119385600-119394400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr3:119385600-119394600	Strong transcription	Monocytes-CD14+_RO01746	blood
48	chr3:119385800-119390600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr3:119385800-119391200	Strong transcription	Duodenum Smooth Muscle	Duodenum
50	chr3:119385800-119394000	Strong transcription	Breast Myoepithelial Primary Cells	Breast

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