Variant report

Variant	rs4440453
Chromosome Location	chr6:25409846-25409847
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:25409840..25412613-chr6:25418004..25420137,2	K562	blood:

Extended variants
information (count: 12 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs17317669	0.85[CEU][hapmap];0.93[MEX][hapmap]
rs4368803	0.86[CHD][hapmap];1.00[JPT][hapmap]
rs9358854	0.93[JPT][hapmap]
rs9366619	0.85[CEU][hapmap]
rs9366621	1.00[ASW][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes]
rs9379762	0.93[JPT][hapmap]
rs9379763	0.85[AMR][1000 genomes]

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	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
4	nsv830612	chr6:25342408-25509758	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	esv1850810	chr6:25405576-25462543	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4440453	ZKSCAN3	cis	cerebellum	SCAN

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25377400-25410600	Weak transcription	Gastric	stomach
2	chr6:25403800-25410600	Weak transcription	Pancreas	Pancrea
3	chr6:25404400-25410800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
4	chr6:25405200-25413200	Weak transcription	Fetal Lung	lung
5	chr6:25405800-25410400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr6:25405800-25410600	Enhancers	Primary T helper cells fromperipheralblood	blood
7	chr6:25405800-25411600	Enhancers	Fetal Thymus	thymus
8	chr6:25405800-25412600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr6:25406000-25410600	Weak transcription	Fetal Intestine Small	intestine
10	chr6:25406000-25413200	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr6:25406200-25410000	Enhancers	H1 Cell Line	embryonic stem cell
12	chr6:25406200-25410400	Enhancers	Primary T helper cells PMA-I stimulated	--
13	chr6:25406200-25410600	Enhancers	Primary T killer memory cells from peripheral blood	blood
14	chr6:25406200-25410600	Weak transcription	Fetal Intestine Large	intestine
15	chr6:25406200-25411600	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr6:25406400-25410400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr6:25406400-25410400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
18	chr6:25406400-25420200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr6:25406600-25410400	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr6:25406600-25410600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr6:25406600-25410600	Weak transcription	Adipose Nuclei	Adipose
22	chr6:25406600-25410600	Weak transcription	NHEK	skin
23	chr6:25406600-25410800	Weak transcription	Lung	lung
24	chr6:25406600-25411600	Weak transcription	Colonic Mucosa	Colon
25	chr6:25406800-25410400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr6:25406800-25410600	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr6:25407000-25410200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr6:25407000-25410400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr6:25407200-25410000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr6:25407200-25410200	Weak transcription	Primary hematopoietic stem cells	blood
31	chr6:25407200-25410600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr6:25407200-25413200	Weak transcription	Spleen	Spleen
33	chr6:25407200-25420200	Weak transcription	Monocytes-CD14+_RO01746	blood
34	chr6:25407800-25410600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr6:25407800-25412600	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr6:25408000-25410400	Weak transcription	Duodenum Mucosa	Duodenum
37	chr6:25408000-25410400	Weak transcription	GM12878-XiMat	blood
38	chr6:25408000-25410600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr6:25408000-25413200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr6:25408200-25410400	Weak transcription	Primary T cells from cord blood	blood
41	chr6:25408200-25410600	Weak transcription	Right Atrium	heart
42	chr6:25408200-25411800	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr6:25408200-25412800	Weak transcription	Aorta	Aorta
44	chr6:25408200-25413000	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr6:25408400-25411600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr6:25408400-25413000	Weak transcription	HUES64 Cell Line	embryonic stem cell
47	chr6:25408400-25413200	Weak transcription	Fetal Muscle Leg	muscle
48	chr6:25408400-25415400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr6:25408400-25416000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr6:25408600-25410400	Weak transcription	Thymus	Thymus

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