Variant report

Variant	rs4899244
Chromosome Location	chr14:68959711-68959712
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:68958868..68960995-chr14:69252275..69254808,2	MCF-7	breast:
2	chr14:68958814..68961806-chr14:68963005..68965065,2	K562	blood:
3	chr14:68953391..68956250-chr14:68958714..68961472,3	MCF-7	breast:
4	chr14:68957700..68966900-chr14:68968037..68976020,15	MCF-7	breast:
5	chr14:68957189..68962665-chr14:69258217..69261056,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000185650	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs12587231	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12590642	0.80[ASN][1000 genomes]
rs2074562	0.84[GIH][hapmap]
rs2331706	0.82[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap]
rs2525510	0.82[CEU][hapmap];0.89[JPT][hapmap];0.81[EUR][1000 genomes]
rs2717217	0.84[GIH][hapmap]
rs3784130	0.95[JPT][hapmap]
rs3784131	0.84[CHD][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs737387	0.82[CEU][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes]
rs739872	0.81[EUR][1000 genomes]
rs765899	1.00[GIH][hapmap];0.95[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869154	chr14:68366754-69041768	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4899244	FAM71D	cis	parietal	SCAN
rs4899244	SLC39A9	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:68944400-68968200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr14:68950600-68968200	Weak transcription	Gastric	stomach
3	chr14:68951000-68969400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr14:68951800-68960400	Weak transcription	Colon Smooth Muscle	Colon
5	chr14:68952000-68961800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr14:68952000-68967600	Weak transcription	Thymus	Thymus
7	chr14:68952400-68960600	Weak transcription	Primary T cells from cord blood	blood
8	chr14:68953200-68960400	Weak transcription	Fetal Lung	lung
9	chr14:68953400-68960200	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr14:68954000-68961600	Weak transcription	Lung	lung
11	chr14:68955000-68961000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr14:68955200-68961000	Weak transcription	Fetal Thymus	thymus
13	chr14:68955200-68961200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr14:68955200-68961800	Weak transcription	HSMM	muscle
15	chr14:68955200-68967600	Weak transcription	Placenta	Placenta
16	chr14:68955400-68961200	Weak transcription	NHEK	skin
17	chr14:68955400-68961400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr14:68955400-68967600	Weak transcription	Pancreas	Pancrea
19	chr14:68956200-68960800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
20	chr14:68956800-68971800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr14:68957400-68960200	Enhancers	Fetal Intestine Large	intestine
22	chr14:68957400-68960200	Enhancers	Fetal Intestine Small	intestine
23	chr14:68957600-68965600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr14:68957800-68959800	Weak transcription	Fetal Muscle Leg	muscle
25	chr14:68958000-68959800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr14:68958000-68961400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr14:68958000-68961800	Weak transcription	Spleen	Spleen
28	chr14:68958200-68959800	Enhancers	GM12878-XiMat	blood
29	chr14:68958200-68962000	Enhancers	Fetal Stomach	stomach
30	chr14:68958400-68960000	Enhancers	Primary B cells from peripheral blood	blood
31	chr14:68958600-68960000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr14:68958600-68960000	Enhancers	HUES48 Cell Line	embryonic stem cell
33	chr14:68958600-68967800	Weak transcription	Ovary	ovary
34	chr14:68958800-68960400	Enhancers	iPS-18 Cell Line	embryonic stem cell
35	chr14:68959000-68960400	Enhancers	iPS-20b Cell Line	embryonic stem cell
36	chr14:68959200-68959800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr14:68959200-68960400	Enhancers	H1 Cell Line	embryonic stem cell
38	chr14:68959200-68960400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr14:68959200-68960400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr14:68959200-68960400	Enhancers	iPS-15b Cell Line	embryonic stem cell
41	chr14:68959200-68960600	Enhancers	ES-I3 Cell Line	embryonic stem cell
42	chr14:68959200-68960600	Enhancers	H9 Cell Line	embryonic stem cell
43	chr14:68959400-68959800	Enhancers	Cortex derived primary cultured neurospheres	brain
44	chr14:68959400-68960400	Enhancers	HUES6 Cell Line	embryonic stem cell
45	chr14:68959400-68960400	Enhancers	HUES64 Cell Line	embryonic stem cell
46	chr14:68959400-68960600	Enhancers	Fetal Kidney	kidney
47	chr14:68959400-68963400	Enhancers	Placenta Amnion	Placenta Amnion
48	chr14:68959600-68960200	Enhancers	Primary B cells from cord blood	blood
49	chr14:68959600-68960200	Enhancers	Fetal Muscle Trunk	muscle
50	chr14:68959600-68961200	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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