Variant report

Variant	rs1872294
Chromosome Location	chr4:143232702-143232703
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:143232269..143234234-chr4:143236195..143238233,2	K562	blood:

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1872292	0.94[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1872293	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1872295	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2646095	0.84[CEU][hapmap]
rs34706232	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3775699	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3775700	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3775701	0.89[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3822154	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6831744	0.94[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6858270	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs960678	0.83[CHD][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	nsv498005	chr4:142515689-143502988	Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv1027781	chr4:142943485-143306567	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv830098	chr4:143050143-143234384	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv830099	chr4:143138257-143285055	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv830100	chr4:143216951-143393305	Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1872294	SCOC	cis	parietal	SCAN

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:143200000-143240000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr4:143204600-143233600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr4:143206000-143233400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr4:143210800-143235400	Weak transcription	Right Ventricle	heart
5	chr4:143215200-143235200	Weak transcription	Osteobl	bone
6	chr4:143215800-143235200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr4:143216200-143234600	Weak transcription	Thymus	Thymus
8	chr4:143216600-143233600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr4:143217600-143238600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr4:143217600-143260800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr4:143218200-143233400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr4:143218800-143234600	Weak transcription	Duodenum Mucosa	Duodenum
13	chr4:143219200-143233600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr4:143219400-143236600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr4:143220600-143233000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr4:143221600-143234800	Weak transcription	Pancreas	Pancrea
17	chr4:143221800-143233000	Weak transcription	Primary hematopoietic stem cells	blood
18	chr4:143222600-143233800	Strong transcription	Primary T cells fromperipheralblood	blood
19	chr4:143223600-143239200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr4:143224400-143234800	Strong transcription	Dnd41	blood
21	chr4:143225200-143235800	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr4:143225400-143237400	Weak transcription	Ovary	ovary
23	chr4:143225400-143240200	Weak transcription	Esophagus	oesophagus
24	chr4:143225800-143233200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr4:143225800-143234600	Weak transcription	NHDF-Ad	bronchial
26	chr4:143227200-143233200	Weak transcription	Brain Hippocampus Middle	brain
27	chr4:143227400-143233800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr4:143228000-143233800	Strong transcription	Primary T helper cells PMA-I stimulated	--
29	chr4:143228800-143234600	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr4:143229000-143235600	Strong transcription	NHEK	skin
31	chr4:143229200-143233600	Weak transcription	Aorta	Aorta
32	chr4:143229200-143233800	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr4:143229400-143232800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr4:143229400-143234600	Weak transcription	Small Intestine	intestine
35	chr4:143229400-143235600	Weak transcription	Rectal Smooth Muscle	rectum
36	chr4:143229600-143234600	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr4:143230200-143233400	Weak transcription	Stomach Smooth Muscle	stomach
38	chr4:143231000-143235000	Weak transcription	Fetal Intestine Small	intestine
39	chr4:143231200-143233200	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr4:143231200-143233600	Weak transcription	Left Ventricle	heart
41	chr4:143231200-143234200	Strong transcription	Primary T helper cells fromperipheralblood	blood
42	chr4:143231200-143234400	Weak transcription	Fetal Intestine Large	intestine
43	chr4:143231200-143235400	Weak transcription	Gastric	stomach
44	chr4:143231200-143235400	Weak transcription	Psoas Muscle	Psoas
45	chr4:143231400-143232800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr4:143231400-143233000	Weak transcription	Fetal Muscle Leg	muscle
47	chr4:143231400-143233200	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr4:143231400-143234000	Weak transcription	Fetal Heart	heart
49	chr4:143231400-143234200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
50	chr4:143231400-143239400	Weak transcription	HSMMtube	muscle

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