Variant report

Variant	rs4899246
Chromosome Location	chr14:69060202-69060203
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:69059475..69061008-chr14:69062632..69064559,2	K562	blood:
2	chr14:69059806..69062420-chr14:69100843..69102617,2	MCF-7	breast:
3	chr14:69059250..69061787-chr14:69065099..69067074,2	K562	blood:
4	chr14:69058975..69063835-chr14:69063915..69067303,5	MCF-7	breast:

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs12878761	0.90[CEU][hapmap];0.85[JPT][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12894230	0.89[CEU][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1547012	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17829341	0.85[JPT][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2256983	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs2256988	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs2256994	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs2257000	0.87[AFR][1000 genomes]
rs2257001	0.92[AFR][1000 genomes]
rs2257007	0.92[AFR][1000 genomes]
rs2257014	0.94[LWK][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs2257021	0.92[AFR][1000 genomes]
rs2257111	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[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];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2257116	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36035347	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4531674	0.90[CEU][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs4902604	0.81[CEU][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.85[JPT][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59934413	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61985819	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61985820	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61985824	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61985825	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[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	nsv832822	chr14:68874640-69060272	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	esv1795754	chr14:69017623-69079110	Enhancers Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	esv1832715	chr14:69017623-69079110	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4899246	MPP5	cis	parietal	SCAN
rs4899246	PLEKHG3	cis	cerebellum	SCAN

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:69049800-69064000	Enhancers	Fetal Muscle Leg	muscle
2	chr14:69051200-69061800	Enhancers	Fetal Stomach	stomach
3	chr14:69052600-69060400	Weak transcription	Osteobl	bone
4	chr14:69052800-69064800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr14:69053400-69064800	Weak transcription	Brain Substantia Nigra	brain
6	chr14:69054200-69063400	Weak transcription	Small Intestine	intestine
7	chr14:69054400-69060400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr14:69054600-69060400	Weak transcription	Fetal Brain Male	brain
9	chr14:69054600-69061000	Weak transcription	NHEK	skin
10	chr14:69054800-69060600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr14:69054800-69060600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr14:69054800-69061400	Enhancers	Rectal Smooth Muscle	rectum
13	chr14:69055200-69060400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr14:69056000-69061000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr14:69056200-69060400	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr14:69056400-69060400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr14:69056600-69060400	Weak transcription	NH-A	brain
18	chr14:69056800-69060400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr14:69056800-69060400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr14:69057000-69060400	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr14:69057000-69060400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr14:69057000-69060600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr14:69057000-69061400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr14:69057000-69065800	Weak transcription	Gastric	stomach
25	chr14:69057200-69060400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr14:69057200-69060400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr14:69057200-69060600	Weak transcription	Fetal Heart	heart
28	chr14:69057200-69063000	Weak transcription	Stomach Mucosa	stomach
29	chr14:69057200-69063400	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr14:69057400-69060400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr14:69057400-69060400	Weak transcription	Fetal Intestine Large	intestine
32	chr14:69057400-69060400	Weak transcription	NHLF	lung
33	chr14:69057400-69060600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr14:69057400-69061400	Weak transcription	Psoas Muscle	Psoas
35	chr14:69057400-69064600	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr14:69057600-69063400	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr14:69057600-69063400	Weak transcription	Right Atrium	heart
38	chr14:69057600-69065200	Weak transcription	Lung	lung
39	chr14:69057600-69065800	Weak transcription	Left Ventricle	heart
40	chr14:69057800-69060400	Weak transcription	Fetal Intestine Small	intestine
41	chr14:69057800-69061000	Weak transcription	Pancreas	Pancrea
42	chr14:69057800-69064800	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr14:69058000-69060400	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr14:69058200-69061400	Enhancers	Colon Smooth Muscle	Colon
45	chr14:69058600-69062200	Enhancers	Fetal Kidney	kidney
46	chr14:69058600-69065200	Weak transcription	Esophagus	oesophagus
47	chr14:69058800-69065000	Weak transcription	Ovary	ovary
48	chr14:69059000-69063400	Weak transcription	Right Ventricle	heart
49	chr14:69059200-69061800	Enhancers	Fetal Muscle Trunk	muscle
50	chr14:69059200-69061800	Enhancers	Placenta	Placenta

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