Variant report

Variant	rs16852993
Chromosome Location	chr3:142842321-142842322
allele	G/T
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:5)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:142841180..142845810-chr3:142884202..142887242,4	K562	blood:
2	chr3:142832736..142834624-chr3:142842242..142844343,2	K562	blood:
3	chr3:142729466..142731298-chr3:142840071..142842956,2	K562	blood:
4	chr3:142842312..142844525-chr3:142920222..142922927,2	K562	blood:
5	chr3:142842296..142843845-chr3:142877160..142879229,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CHST2-2	chr3:142842204-142842418	ENSG00000241679

No data

Variant related genes	Relation type
ENSG00000163714	Chromatin interaction
ENSG00000211483	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs13322379	1.00[CEU][hapmap]
rs13322528	1.00[CEU][hapmap];1.00[GIH][hapmap]
rs16852899	1.00[CEU][hapmap]
rs6768278	1.00[CEU][hapmap]
rs6771415	1.00[CEU][hapmap]
rs72994426	1.00[EUR][1000 genomes]
rs72994431	1.00[EUR][1000 genomes]
rs9289653	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs9289655	1.00[EUR][1000 genomes]
rs9881229	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs9990198	1.00[CEU][hapmap];1.00[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877562	chr3:142573789-142846370	Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	esv2757893	chr3:142720230-142962932	Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	esv2759183	chr3:142720230-142964373	Strong transcription Weak transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv949288	chr3:142793323-143585882	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	nsv1007164	chr3:142837004-142891719	Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 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	chr3:142837800-142843400	Active TSS	Fetal Kidney	kidney
2	chr3:142839200-142845800	Transcr. at gene 5' and 3'	Dnd41	blood
3	chr3:142839200-142847200	Transcr. at gene 5' and 3'	Fetal Lung	lung
4	chr3:142839600-142843200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
5	chr3:142840200-142842800	Weak transcription	Liver	Liver
6	chr3:142840200-142843000	Flanking Active TSS	GM12878-XiMat	blood
7	chr3:142840200-142843600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
8	chr3:142840400-142842400	Enhancers	Primary T helper naive cells from peripheral blood	blood
9	chr3:142840400-142843000	Enhancers	Primary hematopoietic stem cells	blood
10	chr3:142840400-142843400	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr3:142840400-142843400	Weak transcription	HSMMtube	muscle
12	chr3:142840400-142843600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr3:142840400-142843600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr3:142840600-142842400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr3:142840600-142842400	Weak transcription	Brain Cingulate Gyrus	brain
16	chr3:142840600-142842600	Enhancers	Primary B cells from peripheral blood	blood
17	chr3:142840600-142842800	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr3:142840600-142843200	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr3:142840600-142843600	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr3:142840600-142845200	Flanking Active TSS	Primary T cells from cord blood	blood
21	chr3:142840600-142854600	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr3:142840800-142843200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr3:142840800-142843600	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr3:142840800-142843600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr3:142840800-142843600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr3:142840800-142843800	Weak transcription	Pancreas	Pancrea
27	chr3:142841000-142842400	Weak transcription	Adipose Nuclei	Adipose
28	chr3:142841000-142842400	Weak transcription	Fetal Brain Female	brain
29	chr3:142841000-142842600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr3:142841000-142842800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr3:142841000-142843600	Weak transcription	HSMM	muscle
32	chr3:142841000-142843800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr3:142841000-142848600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr3:142841200-142843000	Enhancers	Primary hematopoietic stem cells short term culture	blood
35	chr3:142841200-142843600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr3:142841200-142843600	Weak transcription	Brain Angular Gyrus	brain
37	chr3:142841200-142843600	Weak transcription	Gastric	stomach
38	chr3:142841200-142843800	Weak transcription	Lung	lung
39	chr3:142841200-142852800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr3:142841200-142853200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr3:142841200-142858000	Weak transcription	Spleen	Spleen
42	chr3:142841400-142842400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr3:142841400-142842800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
44	chr3:142841400-142843000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
45	chr3:142841400-142843400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr3:142841400-142844600	Active TSS	Fetal Adrenal Gland	Adrenal Gland
47	chr3:142841400-142844600	Active TSS	Fetal Brain Male	brain
48	chr3:142841600-142842400	Active TSS	HUES6 Cell Line	embryonic stem cell
49	chr3:142841600-142842800	Active TSS	Rectal Mucosa Donor 29	rectum
50	chr3:142841600-142843000	Flanking Active TSS	Primary B cells from cord blood	blood

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