Variant report

Variant	rs1025897
Chromosome Location	chr4:16224242-16224243
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:16214985..16216532-chr4:16224088..16226157,2	K562	blood:
2	chr4:16221619..16226314-chr4:16226369..16230057,8	MCF-7	breast:
3	chr4:16207884..16210057-chr4:16223808..16226102,2	K562	blood:
4	chr4:16208002..16209532-chr4:16222968..16225755,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000263327	Chromatin interaction
ENSG00000169762	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10006159	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10019399	0.80[YRI][hapmap]
rs10939657	0.88[ASN][1000 genomes]
rs11730977	0.85[AFR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13133263	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13151111	0.86[ASN][1000 genomes]
rs13634	0.87[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.93[MKK][hapmap];0.85[TSI][hapmap];0.85[YRI][hapmap];0.83[AFR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1618243	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1662654	0.80[YRI][hapmap]
rs16893162	0.94[LWK][hapmap];0.85[YRI][hapmap]
rs1712492	0.87[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.94[LWK][hapmap];0.83[MKK][hapmap];0.82[TSI][hapmap];0.85[YRI][hapmap];0.85[AFR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1712495	0.82[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs178450	0.80[YRI][hapmap]
rs203434	0.93[ASW][hapmap];0.91[CEU][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.86[LWK][hapmap];0.94[MKK][hapmap];0.84[TSI][hapmap];0.80[YRI][hapmap];0.83[AFR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs203435	0.94[JPT][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs317853	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs317854	0.80[YRI][hapmap]
rs317857	0.81[ASN][1000 genomes]
rs317869	0.80[YRI][hapmap]
rs317870	0.80[YRI][hapmap]
rs317872	0.80[YRI][hapmap]
rs317873	0.87[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.97[LWK][hapmap];0.94[MKK][hapmap];0.82[TSI][hapmap];0.85[YRI][hapmap];0.89[AFR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs317875	0.80[YRI][hapmap]
rs317876	0.80[YRI][hapmap]
rs36012247	0.89[AFR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3749543	0.82[ASN][1000 genomes]
rs4317201	0.91[ASN][1000 genomes]
rs6812660	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7666361	0.89[AFR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs961449	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][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	nsv998299	chr4:16031459-16226466	Bivalent/Poised TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
2	nsv1004821	chr4:16055996-16830629	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv537046	chr4:16055996-16830629	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv537047	chr4:16182060-16375787	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv878720	chr4:16222046-16242215	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:16193000-16225800	Weak transcription	Colonic Mucosa	Colon
2	chr4:16193200-16225800	Weak transcription	Fetal Brain Female	brain
3	chr4:16198800-16225600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr4:16198800-16226000	Weak transcription	NHEK	skin
5	chr4:16198800-16226400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr4:16204800-16226600	Weak transcription	NH-A	brain
7	chr4:16205200-16225600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr4:16208400-16224400	Weak transcription	Stomach Smooth Muscle	stomach
9	chr4:16208400-16225200	Weak transcription	Fetal Kidney	kidney
10	chr4:16208400-16225800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr4:16208800-16225600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr4:16208800-16225600	Weak transcription	Esophagus	oesophagus
13	chr4:16208800-16225600	Weak transcription	Gastric	stomach
14	chr4:16208800-16225800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr4:16208800-16225800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr4:16208800-16227200	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr4:16209000-16225600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr4:16209200-16225600	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr4:16209200-16225600	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr4:16209400-16226200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr4:16209400-16226200	Weak transcription	HSMMtube	muscle
22	chr4:16210400-16225800	Weak transcription	Brain Germinal Matrix	brain
23	chr4:16212200-16226000	Weak transcription	NHDF-Ad	bronchial
24	chr4:16214000-16224400	Weak transcription	Brain Anterior Caudate	brain
25	chr4:16214400-16226800	Weak transcription	Fetal Muscle Trunk	muscle
26	chr4:16214600-16224400	Weak transcription	Brain Angular Gyrus	brain
27	chr4:16214600-16225800	Weak transcription	Placenta	Placenta
28	chr4:16214800-16225200	Weak transcription	Hela-S3	cervix
29	chr4:16214800-16225800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr4:16215000-16224600	Weak transcription	Colon Smooth Muscle	Colon
31	chr4:16215000-16226000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr4:16215200-16225000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr4:16215600-16225600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr4:16216200-16225600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr4:16216600-16224400	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr4:16216800-16225600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr4:16218600-16224400	Weak transcription	Small Intestine	intestine
38	chr4:16218600-16224400	Weak transcription	Spleen	Spleen
39	chr4:16218600-16225600	Weak transcription	Lung	lung
40	chr4:16218800-16224400	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr4:16218800-16225200	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr4:16219000-16224400	Weak transcription	Rectal Smooth Muscle	rectum
43	chr4:16219000-16224600	Weak transcription	Brain Cingulate Gyrus	brain
44	chr4:16219600-16224400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr4:16219600-16224600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr4:16219600-16224800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr4:16219600-16225000	Weak transcription	Fetal Muscle Leg	muscle
48	chr4:16219600-16225600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr4:16220200-16224400	Weak transcription	Primary monocytes fromperipheralblood	blood
50	chr4:16221600-16224400	Weak transcription	Psoas Muscle	Psoas

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