Variant report

Variant	rs1344674
Chromosome Location	chr3:141125186-141125187
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:141085122..141087932-chr3:141123780..141125883,2	MCF-7	breast:
2	chr3:141114089..141115848-chr3:141123999..141126481,2	K562	blood:
3	chr3:141104620..141107838-chr3:141124068..141126667,3	MCF-7	breast:
4	chr3:141106458..141109365-chr3:141123758..141125561,2	K562	blood:
5	chr3:141100985..141103697-chr3:141123683..141126510,2	K562	blood:
6	chr3:141123064..141125479-chr3:141137603..141140380,2	MCF-7	breast:
7	chr3:141124961..141126673-chr3:141128452..141131076,2	K562	blood:
8	chr3:141120608..141122904-chr3:141123337..141125352,2	K562	blood:
9	chr3:141088820..141091085-chr3:141123640..141126177,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000177311	Chromatin interaction
ENSG00000249417	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs13068733	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13077048	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1344672	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[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];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1346408	0.81[CEU][hapmap]
rs1582874	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1863868	0.81[CEU][hapmap];0.81[JPT][hapmap]
rs1991431	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2871960	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[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];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4683605	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4683606	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57345461	1.00[ASN][1000 genomes]
rs58473751	1.00[ASN][1000 genomes]
rs6440003	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6440006	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6762826	0.90[JPT][hapmap]
rs6763927	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6763931	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6764769	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6785012	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6802753	0.84[JPT][hapmap]
rs6808936	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs724016	0.91[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7613516	0.81[CEU][hapmap]
rs7624084	0.89[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7625643	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7632381	0.90[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7650602	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9846396	1.00[CEU][hapmap];0.94[GIH][hapmap];0.96[MEX][hapmap];0.80[MKK][hapmap];0.81[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9853018	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9856584	0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv829744	chr3:141016749-141189168	Genic enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1344674	RASA2	cis	cerebellum	SCAN
rs1344674	ZBTB38	cis	cerebellum	SCAN
rs1344674	SPSB4	cis	parietal	SCAN

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:141122000-141127600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr3:141122000-141128600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr3:141122000-141129200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr3:141122000-141130200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:141122000-141131800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr3:141122200-141126200	Genic enhancers	HSMM	muscle
7	chr3:141122200-141128800	Weak transcription	Fetal Thymus	thymus
8	chr3:141122200-141129400	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr3:141122400-141126000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr3:141122400-141126800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr3:141122400-141127000	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
12	chr3:141122400-141127800	Genic enhancers	Placenta	Placenta
13	chr3:141122600-141125400	Genic enhancers	HMEC	breast
14	chr3:141122600-141125800	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr3:141122600-141128200	Strong transcription	Fetal Intestine Large	intestine
16	chr3:141122600-141130400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr3:141122600-141130400	Genic enhancers	NH-A	brain
18	chr3:141122800-141125200	Strong transcription	Liver	Liver
19	chr3:141122800-141125600	Genic enhancers	Hela-S3	cervix
20	chr3:141122800-141126200	Strong transcription	Primary B cells from peripheral blood	blood
21	chr3:141122800-141126600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr3:141122800-141127000	Strong transcription	Primary monocytes fromperipheralblood	blood
23	chr3:141122800-141127600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr3:141122800-141129400	Enhancers	Fetal Heart	heart
25	chr3:141123000-141125200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr3:141123000-141125200	Genic enhancers	Brain Dorsolateral Prefrontal Cortex	brain
27	chr3:141123000-141125600	Strong transcription	Stomach Mucosa	stomach
28	chr3:141123000-141125600	Genic enhancers	HSMMtube	muscle
29	chr3:141123000-141126200	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
30	chr3:141123000-141127000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr3:141123000-141127000	Strong transcription	Fetal Brain Male	brain
32	chr3:141123000-141127200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr3:141123000-141127800	Strong transcription	Monocytes-CD14+_RO01746	blood
34	chr3:141123000-141128000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr3:141123000-141128200	Genic enhancers	A549	lung
36	chr3:141123200-141125200	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr3:141123200-141125400	Strong transcription	Brain Germinal Matrix	brain
38	chr3:141123200-141126000	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
39	chr3:141123200-141129200	Genic enhancers	Primary T cells fromperipheralblood	blood
40	chr3:141123200-141130400	Genic enhancers	Osteobl	bone
41	chr3:141123200-141130600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr3:141123200-141130600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr3:141123400-141125200	Strong transcription	Adipose Nuclei	Adipose
44	chr3:141123400-141125400	Genic enhancers	Primary T helper cells PMA-I stimulated	--
45	chr3:141123400-141125600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr3:141123400-141125800	Genic enhancers	Rectal Mucosa Donor 31	rectum
47	chr3:141123400-141126000	Strong transcription	Primary hematopoietic stem cells	blood
48	chr3:141123400-141126600	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr3:141123400-141127600	Strong transcription	Fetal Stomach	stomach
50	chr3:141123600-141125400	Strong transcription	Brain Substantia Nigra	brain

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