Variant report

Variant	rs16830650
Chromosome Location	chr2:152895198-152895199
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:152888573..152890239-chr2:152893538..152895609,2	MCF-7	breast:
2	chr2:152893970..152895588-chr2:153030561..153032337,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115145	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11893379	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11901937	0.85[YRI][hapmap]
rs11902858	0.83[ASW][hapmap];0.82[LWK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16830649	0.95[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16830656	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16830669	0.87[YRI][hapmap]
rs6711790	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6716430	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6721639	1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6728438	1.00[AMR][1000 genomes]
rs6745868	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6745984	0.91[ASW][hapmap];0.82[LWK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72998994	1.00[AMR][1000 genomes]
rs73000911	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73000931	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73000934	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7569358	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7604560	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005746	chr2:152361972-153059840	Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv535984	chr2:152361972-153059840	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	esv3693431	chr2:152683731-152981827	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv875287	chr2:152714680-153110573	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	nsv875288	chr2:152716628-153183646	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
6	nsv875289	chr2:152720030-153183646	Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
7	nsv875290	chr2:152803129-152920126	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
8	esv1847028	chr2:152863856-153045036	Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16830650	LGALS3BP	trans	lymphoblastoid	seeQTL

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:152890000-152904400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr2:152893400-152895400	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr2:152893400-152895400	Enhancers	Brain Cingulate Gyrus	brain
4	chr2:152893400-152898000	Enhancers	Fetal Stomach	stomach
5	chr2:152893600-152895400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr2:152893600-152895400	Enhancers	HUES48 Cell Line	embryonic stem cell
7	chr2:152893600-152895400	Enhancers	Brain Hippocampus Middle	brain
8	chr2:152893600-152895400	Enhancers	Brain Inferior Temporal Lobe	brain
9	chr2:152893600-152895400	Enhancers	Colon Smooth Muscle	Colon
10	chr2:152893600-152895400	Enhancers	Fetal Kidney	kidney
11	chr2:152893600-152895400	Enhancers	Skeletal Muscle Male	skeletal muscle
12	chr2:152893600-152895600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr2:152893600-152895600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr2:152893600-152895600	Enhancers	Primary hematopoietic stem cells short term culture	blood
15	chr2:152893600-152895600	Enhancers	Adipose Nuclei	Adipose
16	chr2:152893600-152895600	Enhancers	Duodenum Smooth Muscle	Duodenum
17	chr2:152893600-152896000	Enhancers	Rectal Mucosa Donor 31	rectum
18	chr2:152893600-152896200	Enhancers	Fetal Lung	lung
19	chr2:152893600-152896400	Enhancers	Fetal Muscle Leg	muscle
20	chr2:152893800-152895200	Enhancers	Brain Angular Gyrus	brain
21	chr2:152893800-152895400	Enhancers	HUES6 Cell Line	embryonic stem cell
22	chr2:152893800-152895400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr2:152893800-152895400	Enhancers	Rectal Smooth Muscle	rectum
24	chr2:152893800-152895400	Bivalent Enhancer	HepG2	liver
25	chr2:152894000-152895400	Enhancers	iPS-20b Cell Line	embryonic stem cell
26	chr2:152894000-152895400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
27	chr2:152894000-152895400	Enhancers	Duodenum Mucosa	Duodenum
28	chr2:152894000-152895400	Enhancers	Sigmoid Colon	Sigmoid Colon
29	chr2:152894000-152895400	Enhancers	Skeletal Muscle Female	skeletal muscle
30	chr2:152894000-152895600	Enhancers	Cortex derived primary cultured neurospheres	brain
31	chr2:152894200-152895200	Enhancers	Ovary	ovary
32	chr2:152894200-152895400	Enhancers	Primary hematopoietic stem cells	blood
33	chr2:152894200-152895400	Enhancers	Brain Anterior Caudate	brain
34	chr2:152894200-152895400	Enhancers	Placenta	Placenta
35	chr2:152894200-152895600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr2:152894200-152895800	Enhancers	Fetal Muscle Trunk	muscle
37	chr2:152894200-152896400	Enhancers	Fetal Brain Male	brain
38	chr2:152894400-152895200	Enhancers	Liver	Liver
39	chr2:152894400-152895200	Enhancers	Colonic Mucosa	Colon
40	chr2:152894400-152895200	Weak transcription	Right Ventricle	heart
41	chr2:152894400-152895400	Enhancers	Left Ventricle	heart
42	chr2:152894400-152895400	Enhancers	Lung	lung
43	chr2:152894400-152895600	Enhancers	Right Atrium	heart
44	chr2:152894400-152899400	Weak transcription	Fetal Thymus	thymus
45	chr2:152894400-152899600	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr2:152894600-152895200	Enhancers	Monocytes-CD14+_RO01746	blood
47	chr2:152894600-152895400	Enhancers	ES-I3 Cell Line	embryonic stem cell
48	chr2:152894600-152895400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr2:152894600-152895400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
50	chr2:152894600-152895400	Enhancers	Fetal Intestine Large	intestine

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