Variant report

Variant	rs1344223
Chromosome Location	chr4:7931635-7931636
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	chr4:7930429..7933293-chr4:7935968..7937557,2	MCF-7	breast:
2	chr4:7930761..7932557-chr4:7940188..7942388,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000228919	Chromatin interaction
ENSG00000196526	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs12696835	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1557817	0.82[CHB][hapmap]
rs2018399	0.82[CHB][hapmap]
rs2385912	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2385914	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28446696	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34072960	0.82[ASN][1000 genomes]
rs6447872	1.00[JPT][hapmap]
rs66479458	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6827395	0.82[CHB][hapmap]
rs6838291	0.82[CHB][hapmap]
rs6840305	0.90[CEU][hapmap];0.88[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.82[TSI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6846757	0.95[CEU][hapmap];0.85[CHB][hapmap];0.94[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7669433	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7669645	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7695142	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7695170	0.84[CEU][hapmap];0.83[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7698368	0.83[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9993085	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[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	nsv491712	chr4:7582506-8155069	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	esv34140	chr4:7787936-8172491	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
3	esv2754386	chr4:7822449-7992909	Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	esv2756298	chr4:7822449-7992909	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv878578	chr4:7841833-7969594	Enhancers Flanking Active TSS Genic enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1344223	AFAP	cis	multi-tissue	Pritchard
rs1344223	WDR1	cis	cerebellum	SCAN
rs1344223	ABLIM2	cis	cerebellum	SCAN

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:7907800-7935800	Weak transcription	Right Ventricle	heart
2	chr4:7926600-7936600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr4:7926800-7935400	Weak transcription	Fetal Brain Male	brain
4	chr4:7927800-7932400	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr4:7928000-7932000	Enhancers	Stomach Mucosa	stomach
6	chr4:7928200-7932200	Enhancers	Colon Smooth Muscle	Colon
7	chr4:7930000-7932000	Genic enhancers	Fetal Stomach	stomach
8	chr4:7930400-7932000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr4:7930400-7932000	Genic enhancers	Fetal Lung	lung
10	chr4:7930400-7932200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
11	chr4:7930400-7932200	Genic enhancers	Fetal Muscle Trunk	muscle
12	chr4:7930400-7932400	Enhancers	Duodenum Smooth Muscle	Duodenum
13	chr4:7930400-7934000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr4:7930600-7931800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr4:7930600-7931800	Enhancers	HUES64 Cell Line	embryonic stem cell
16	chr4:7930600-7931800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr4:7930600-7931800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr4:7930600-7931800	Enhancers	Adipose Nuclei	Adipose
19	chr4:7930600-7931800	Enhancers	Skeletal Muscle Male	skeletal muscle
20	chr4:7930600-7932000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr4:7930600-7932000	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr4:7930600-7932000	Enhancers	Brain Anterior Caudate	brain
23	chr4:7930600-7932000	Enhancers	Duodenum Mucosa	Duodenum
24	chr4:7930600-7932000	Enhancers	Sigmoid Colon	Sigmoid Colon
25	chr4:7930600-7932000	Enhancers	HSMMtube	muscle
26	chr4:7930600-7932200	Enhancers	H1 Cell Line	embryonic stem cell
27	chr4:7930600-7932200	Enhancers	HUES48 Cell Line	embryonic stem cell
28	chr4:7930600-7932200	Enhancers	Colonic Mucosa	Colon
29	chr4:7930600-7932200	Enhancers	Fetal Muscle Leg	muscle
30	chr4:7930600-7932200	Enhancers	Pancreas	Pancrea
31	chr4:7930600-7932200	Enhancers	Rectal Mucosa Donor 31	rectum
32	chr4:7930600-7932200	Enhancers	HSMM	muscle
33	chr4:7930600-7932400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr4:7930600-7932400	Enhancers	Cortex derived primary cultured neurospheres	brain
35	chr4:7930600-7932400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr4:7930600-7932400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr4:7930600-7932400	Enhancers	Esophagus	oesophagus
38	chr4:7930600-7932600	Enhancers	Primary T helper cells fromperipheralblood	blood
39	chr4:7930600-7932600	Enhancers	Placenta	Placenta
40	chr4:7930600-7935600	Genic enhancers	Osteobl	bone
41	chr4:7930800-7932000	Enhancers	iPS-15b Cell Line	embryonic stem cell
42	chr4:7930800-7932000	Enhancers	iPS-18 Cell Line	embryonic stem cell
43	chr4:7930800-7932000	Enhancers	Small Intestine	intestine
44	chr4:7930800-7932200	Enhancers	Placenta Amnion	Placenta Amnion
45	chr4:7930800-7932400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr4:7930800-7932400	Enhancers	HUES6 Cell Line	embryonic stem cell
47	chr4:7930800-7932400	Enhancers	HMEC	breast
48	chr4:7931000-7931800	Flanking Active TSS	NHEK	skin
49	chr4:7931000-7932000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr4:7931000-7932000	Enhancers	iPS-20b Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links