Variant report

Variant	rs3217840
Chromosome Location	chr12:4394877-4394878
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	chr12:4007431..4009689-chr12:4393873..4396492,2	K562	blood:
2	chr12:4393589..4397417-chr12:4408802..4414196,5	K562	blood:

Variant related genes	Relation type
ENSG00000256862	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs3217820	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3217830	0.83[ASW][hapmap];0.92[CEU][hapmap];0.86[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3217896	0.84[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.82[TSI][hapmap]
rs3217898	0.88[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap]
rs4372527	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530520	chr12:3726841-4601757	Enhancers Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv832317	chr12:4315298-4435615	Enhancers Strong transcription Genic enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv541361	chr12:4362258-4413849	Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv437722	chr12:4391332-4396746	ZNF genes & repeats Genic enhancers Strong transcription Enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3217840	EMG1	cis	parietal	SCAN
rs3217840	WDFY3	trans	cerebellum	SCAN

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:4385400-4400000	Transcr. at gene 5' and 3'	Fetal Brain Female	brain
2	chr12:4385400-4404400	Transcr. at gene 5' and 3'	Brain Germinal Matrix	brain
3	chr12:4385600-4400600	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
4	chr12:4385800-4398400	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr12:4386000-4400000	Genic enhancers	Fetal Stomach	stomach
6	chr12:4386000-4404600	Genic enhancers	Primary T cells fromperipheralblood	blood
7	chr12:4386200-4403000	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr12:4386200-4404200	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
9	chr12:4386200-4404800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
10	chr12:4386600-4395000	Strong transcription	Primary B cells from peripheral blood	blood
11	chr12:4386600-4400000	Genic enhancers	Fetal Muscle Leg	muscle
12	chr12:4386600-4406800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr12:4386800-4396200	Strong transcription	Esophagus	oesophagus
14	chr12:4387000-4395000	Strong transcription	Primary B cells from cord blood	blood
15	chr12:4387000-4402600	Genic enhancers	Primary T helper cells PMA-I stimulated	--
16	chr12:4387200-4400000	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr12:4387200-4415200	Strong transcription	H9 Cell Line	embryonic stem cell
18	chr12:4387800-4402400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
19	chr12:4387800-4415200	Strong transcription	HUES64 Cell Line	embryonic stem cell
20	chr12:4388200-4396800	Strong transcription	Fetal Thymus	thymus
21	chr12:4388200-4401000	Genic enhancers	Left Ventricle	heart
22	chr12:4388200-4411200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr12:4388200-4415200	Strong transcription	H1 Cell Line	embryonic stem cell
24	chr12:4388200-4415200	Strong transcription	HUES6 Cell Line	embryonic stem cell
25	chr12:4389200-4400800	Strong transcription	ES-I3 Cell Line	embryonic stem cell
26	chr12:4389400-4396400	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr12:4389600-4403200	Strong transcription	HUES48 Cell Line	embryonic stem cell
28	chr12:4389800-4396600	Strong transcription	NHEK	skin
29	chr12:4390000-4396400	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
30	chr12:4390000-4398400	Genic enhancers	Duodenum Smooth Muscle	Duodenum
31	chr12:4390000-4399600	Genic enhancers	Fetal Intestine Small	intestine
32	chr12:4390000-4405800	Genic enhancers	Cortex derived primary cultured neurospheres	brain
33	chr12:4390200-4399600	Genic enhancers	Fetal Intestine Large	intestine
34	chr12:4390200-4400000	Genic enhancers	Right Ventricle	heart
35	chr12:4390400-4396800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr12:4390400-4397000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
37	chr12:4390400-4397400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr12:4390400-4398200	Genic enhancers	Duodenum Mucosa	Duodenum
39	chr12:4390600-4395000	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr12:4390600-4395600	Genic enhancers	Colon Smooth Muscle	Colon
41	chr12:4390600-4396000	Strong transcription	Placenta Amnion	Placenta Amnion
42	chr12:4390800-4395400	Strong transcription	Colonic Mucosa	Colon
43	chr12:4390800-4395600	Strong transcription	Rectal Mucosa Donor 31	rectum
44	chr12:4390800-4396000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr12:4390800-4396200	Strong transcription	Lung	lung
46	chr12:4390800-4398800	Genic enhancers	GM12878-XiMat	blood
47	chr12:4390800-4400200	Strong transcription	Fetal Lung	lung
48	chr12:4391000-4395600	Weak transcription	Right Atrium	heart
49	chr12:4391000-4396000	Strong transcription	Rectal Mucosa Donor 29	rectum
50	chr12:4391000-4396200	Strong transcription	Sigmoid Colon	Sigmoid Colon

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