Variant report

Variant	rs16890409
Chromosome Location	chr6:25341553-25341554
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs12192517	0.81[CHD][hapmap];0.83[JPT][hapmap];0.86[ASN][1000 genomes]
rs12193883	0.89[CHB][hapmap];0.83[CHD][hapmap];0.83[JPT][hapmap];0.88[ASN][1000 genomes]
rs12203031	1.00[ASW][hapmap]
rs12211739	1.00[ASW][hapmap]
rs1569558	0.89[CHB][hapmap];0.83[JPT][hapmap];0.89[ASN][1000 genomes]
rs16890474	0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs2328853	0.81[ASN][1000 genomes]
rs34283429	0.89[ASN][1000 genomes]
rs4712910	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4712911	0.91[ASN][1000 genomes]
rs4712916	0.81[ASN][1000 genomes]
rs4712917	0.81[ASN][1000 genomes]
rs4712918	0.84[ASN][1000 genomes]
rs5013971	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9348673	0.86[ASN][1000 genomes]
rs9393641	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv883485	chr6:25259137-25437986	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv883486	chr6:25260434-25422369	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv883487	chr6:25280119-25508868	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs16890409	ZSCAN12	cis	cerebellum	SCAN
rs16890409	BTN2A3	cis	cerebellum	SCAN

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25331800-25341800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr6:25332000-25342400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr6:25332000-25342600	Weak transcription	Primary T helper cells PMA-I stimulated	--
4	chr6:25332000-25342600	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr6:25332000-25346800	Weak transcription	Ovary	ovary
6	chr6:25333200-25343800	Enhancers	Fetal Intestine Small	intestine
7	chr6:25333800-25346400	Weak transcription	Left Ventricle	heart
8	chr6:25334400-25342000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr6:25335200-25359800	Weak transcription	Thymus	Thymus
10	chr6:25335400-25342600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr6:25336400-25342800	Enhancers	Rectal Mucosa Donor 31	rectum
12	chr6:25336800-25342400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr6:25336800-25342600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr6:25336800-25344000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr6:25336800-25350200	Weak transcription	Lung	lung
16	chr6:25336800-25354600	Weak transcription	Right Atrium	heart
17	chr6:25337000-25342800	Weak transcription	Primary T cells from cord blood	blood
18	chr6:25337000-25343200	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr6:25337400-25357800	Weak transcription	NHEK	skin
20	chr6:25337600-25343800	Enhancers	Fetal Intestine Large	intestine
21	chr6:25337800-25342600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr6:25338000-25342400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr6:25338000-25342600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr6:25338800-25343000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr6:25339600-25342000	Enhancers	HUES48 Cell Line	embryonic stem cell
26	chr6:25339600-25346200	Weak transcription	Fetal Lung	lung
27	chr6:25340000-25342000	Weak transcription	Small Intestine	intestine
28	chr6:25340000-25343000	Enhancers	Rectal Mucosa Donor 29	rectum
29	chr6:25340000-25349400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr6:25340400-25343600	Enhancers	Cortex derived primary cultured neurospheres	brain
31	chr6:25340400-25344000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
32	chr6:25340600-25342600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr6:25340600-25342800	Enhancers	H1 Cell Line	embryonic stem cell
34	chr6:25340800-25341600	Enhancers	Stomach Mucosa	stomach
35	chr6:25340800-25342000	Enhancers	iPS-18 Cell Line	embryonic stem cell
36	chr6:25340800-25343400	Enhancers	ES-I3 Cell Line	embryonic stem cell
37	chr6:25340800-25344800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr6:25341000-25342000	Enhancers	HUES6 Cell Line	embryonic stem cell
39	chr6:25341000-25342200	Weak transcription	Colonic Mucosa	Colon
40	chr6:25341000-25343400	Enhancers	HUES64 Cell Line	embryonic stem cell
41	chr6:25341000-25343800	Enhancers	iPS-15b Cell Line	embryonic stem cell
42	chr6:25341000-25352800	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr6:25341000-25359400	Weak transcription	Pancreas	Pancrea
44	chr6:25341200-25342000	Enhancers	iPS-20b Cell Line	embryonic stem cell
45	chr6:25341200-25343000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
46	chr6:25341200-25343000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr6:25341400-25341600	Flanking Active TSS	Duodenum Mucosa	Duodenum
48	chr6:25341400-25342000	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr6:25341400-25342000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr6:25341400-25342200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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