Variant report

Variant	rs2394102
Chromosome Location	chr6:28512017-28512018
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:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:28511881..28516576-chr6:28517392..28521415,6	K562	blood:
2	chr6:28511658..28513836-chr6:28633626..28636236,2	K562	blood:
3	chr6:28508365..28512579-chr6:28582414..28584502,4	K562	blood:
4	chr6:28510237..28512040-chr6:28576892..28578404,2	K562	blood:
5	chr6:28364273..28366438-chr6:28510597..28512229,2	K562	blood:
6	chr6:28510221..28512274-chr6:28527181..28528821,2	K562	blood:
7	chr6:28508074..28513880-chr6:28531341..28537609,9	K562	blood:
8	chr6:28509624..28513880-chr6:28531310..28536044,4	K562	blood:
9	chr6:28367674..28369905-chr6:28510832..28512890,2	K562	blood:
10	chr6:28508618..28512579-chr6:28580487..28584134,6	K562	blood:
11	chr6:28511955..28518467-chr6:28519043..28523058,10	K562	blood:
12	chr6:28510133..28512590-chr6:28554507..28556682,2	MCF-7	breast:
13	chr6:28470071..28472229-chr6:28510465..28513041,2	K562	blood:
14	chr6:28510407..28512273-chr6:28513492..28515889,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000246350	Chromatin interaction
ENSG00000232040	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1005126	0.82[CHB][hapmap]
rs11751928	0.82[CHB][hapmap]
rs13190937	0.82[CHB][hapmap];0.95[CHD][hapmap]
rs13196606	0.82[CHB][hapmap];0.91[CHD][hapmap]
rs13199081	0.82[CHB][hapmap]
rs13215054	0.81[ASN][1000 genomes]
rs13215804	0.82[CHB][hapmap];0.81[CHD][hapmap]
rs13217047	0.81[ASN][1000 genomes]
rs1474589	0.89[CEU][hapmap]
rs17336532	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2232422	0.89[CEU][hapmap];0.80[EUR][1000 genomes]
rs35257859	0.81[ASN][1000 genomes]
rs3799499	0.87[CHD][hapmap]
rs3799500	0.82[CHB][hapmap]
rs41270599	0.83[ASN][1000 genomes]
rs6902687	0.81[CHB][hapmap]
rs6905380	0.82[CHB][hapmap]
rs7754960	0.82[CHB][hapmap]
rs7774981	0.82[CHB][hapmap];0.91[CHD][hapmap]
rs9468358	0.82[CHB][hapmap]

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	nsv462666	chr6:28417222-28574415	Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv601210	chr6:28417222-28574415	Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv1020689	chr6:28449137-28635171	Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
4	nsv830621	chr6:28473951-28675709	Bivalent/Poised TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
5	nsv601211	chr6:28483482-28521316	Bivalent Enhancer Active TSS Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
6	nsv435838	chr6:28507880-28514263	Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2394102	ZSCAN23	cis	cerebellum	SCAN
rs2394102	ZNF323	cis	parietal	SCAN
rs2394102	ZSCAN23	cis	parietal	SCAN

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28509600-28512800	Active TSS	H1 Cell Line	embryonic stem cell
2	chr6:28509800-28512200	Active TSS	A549	lung
3	chr6:28509800-28512600	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr6:28509800-28512600	Active TSS	HUES48 Cell Line	embryonic stem cell
5	chr6:28509800-28512600	Active TSS	HUES64 Cell Line	embryonic stem cell
6	chr6:28509800-28512600	Active TSS	iPS-20b Cell Line	embryonic stem cell
7	chr6:28509800-28512800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr6:28509800-28512800	Active TSS	HUES6 Cell Line	embryonic stem cell
9	chr6:28509800-28512800	Active TSS	iPS-15b Cell Line	embryonic stem cell
10	chr6:28510000-28512200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
11	chr6:28510000-28512200	Active TSS	Fetal Intestine Large	intestine
12	chr6:28510000-28512400	Active TSS	H9 Cell Line	embryonic stem cell
13	chr6:28510000-28512400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr6:28510000-28512400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr6:28510000-28512400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr6:28510000-28512600	Active TSS	Fetal Kidney	kidney
17	chr6:28510000-28512800	Active TSS	iPS-18 Cell Line	embryonic stem cell
18	chr6:28510200-28512200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr6:28510200-28512200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr6:28510200-28512200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr6:28510200-28512200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr6:28510200-28512400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr6:28510200-28512400	Active TSS	Fetal Lung	lung
24	chr6:28510200-28512800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr6:28510400-28512200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr6:28510400-28512200	Bivalent/Poised TSS	Primary mononuclear cells fromperipheralblood	Blood
27	chr6:28510400-28512400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr6:28510800-28512200	Bivalent Enhancer	Primary B cells from peripheral blood	blood
29	chr6:28510800-28512200	Active TSS	Brain Hippocampus Middle	brain
30	chr6:28510800-28512200	Bivalent/Poised TSS	Fetal Stomach	stomach
31	chr6:28510800-28512600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr6:28510800-28521600	Weak transcription	Pancreas	Pancrea
33	chr6:28511000-28512200	Flanking Active TSS	Primary hematopoietic stem cells	blood
34	chr6:28511000-28512200	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
35	chr6:28511200-28512200	Flanking Bivalent TSS/Enh	Primary T cells from cord blood	blood
36	chr6:28511200-28512200	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
37	chr6:28511200-28512200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
38	chr6:28511200-28512200	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
39	chr6:28511200-28512200	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
40	chr6:28511200-28512200	Flanking Bivalent TSS/Enh	HepG2	liver
41	chr6:28511200-28512200	Flanking Active TSS	HUVEC	blood vessel
42	chr6:28511200-28512200	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
43	chr6:28511200-28512200	Active TSS	NHDF-Ad	bronchial
44	chr6:28511400-28512200	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr6:28511400-28512200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr6:28511400-28512200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr6:28511400-28512200	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
48	chr6:28511400-28512200	Bivalent Enhancer	Duodenum Smooth Muscle	Duodenum
49	chr6:28511400-28512200	Active TSS	Osteobl	bone
50	chr6:28511600-28512200	Bivalent/Poised TSS	Primary T killer naive cells fromperipheralblood	blood

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