Variant report

Variant	rs9849038
Chromosome Location	chr3:49771990-49771991
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:49763340..49765220-chr3:49771723..49774304,2	MCF-7	breast:

Extended variants
information (count: 49 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10452032	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs1078341	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs10865956	1.00[CHD][hapmap]
rs11130208	0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap]
rs11130211	0.94[CEU][hapmap]
rs11130217	0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs11709734	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs11720705	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs12637313	0.88[CEU][hapmap];1.00[CHD][hapmap];0.83[TSI][hapmap]
rs12715437	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs1352889	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs1491983	0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap]
rs1491985	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs1532204	0.94[CEU][hapmap]
rs1586827	1.00[CEU][hapmap]
rs1982861	1.00[CHD][hapmap]
rs1996663	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs1996664	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs2029591	0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap]
rs2131108	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs2312462	1.00[CHD][hapmap]
rs2329021	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs3020779	1.00[CEU][hapmap]
rs34890793	0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap]
rs4241405	0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap]
rs4241407	1.00[CHD][hapmap]
rs4855833	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs4855845	1.00[CEU][hapmap]
rs4855846	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs4855882	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs4855885	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs6446285	0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap]
rs6774202	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs6797299	0.94[CEU][hapmap]
rs6809879	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs7613603	1.00[CEU][hapmap]
rs7620848	1.00[CEU][hapmap]
rs7628207	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs7637711	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs9824435	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs9829155	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs9830730	1.00[CEU][hapmap]
rs9835157	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs9862534	1.00[CHD][hapmap]
rs9870755	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs9870858	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap]
rs9883000	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][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	esv1796352	chr3:49687101-49949959	Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription 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 miRNA target site	90 gene(s)	inside rSNPs	diseases
2	nsv967216	chr3:49764885-49776535	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Enhancers	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs9849038	DALRD3	cis	cerebellum	SCAN
rs9849038	RBM6	cis	cerebellum	SCAN
rs9849038	ZNF589	cis	parietal	SCAN
rs9849038	AMT	cis	parietal	SCAN
rs9849038	OR9G4	trans	parietal	SCAN
rs9849038	P4HTM	cis	parietal	SCAN
rs9849038	RNF123	cis	parietal	SCAN
rs9849038	WDR6	cis	cerebellum	SCAN
rs9849038	GNL3	cis	cerebellum	SCAN
rs9849038	DALRD3	cis	parietal	SCAN
rs9849038	ITIH3	cis	cerebellum	SCAN
rs9849038	GMPPB	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49762000-49773800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:49762000-49775000	Weak transcription	Psoas Muscle	Psoas
3	chr3:49762000-49778000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr3:49762400-49772200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr3:49762400-49773000	Weak transcription	Fetal Heart	heart
6	chr3:49762400-49776800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr3:49762400-49781600	Strong transcription	Fetal Stomach	stomach
8	chr3:49762600-49774600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr3:49762600-49776400	Strong transcription	Fetal Brain Female	brain
10	chr3:49762600-49776800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr3:49762600-49777000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr3:49762600-49777200	Strong transcription	Primary neutrophils fromperipheralblood	blood
13	chr3:49762600-49777600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
14	chr3:49762600-49781800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr3:49762600-49785200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr3:49762600-49809000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr3:49762800-49775600	Strong transcription	Fetal Thymus	thymus
18	chr3:49762800-49776400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
19	chr3:49762800-49776600	Strong transcription	Cortex derived primary cultured neurospheres	brain
20	chr3:49763000-49776400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr3:49763000-49776600	Strong transcription	Placenta	Placenta
22	chr3:49763000-49776800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr3:49763000-49784800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr3:49763200-49776400	Strong transcription	Dnd41	blood
25	chr3:49763400-49773600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr3:49764000-49776000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr3:49764000-49776400	Strong transcription	Rectal Mucosa Donor 29	rectum
28	chr3:49764000-49781800	Strong transcription	Fetal Muscle Leg	muscle
29	chr3:49764200-49776600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
30	chr3:49764200-49776600	Strong transcription	Primary T cells from cord blood	blood
31	chr3:49764800-49776600	Strong transcription	Fetal Muscle Trunk	muscle
32	chr3:49765800-49772000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr3:49765800-49775200	Weak transcription	Stomach Mucosa	stomach
34	chr3:49765800-49775400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr3:49765800-49785800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr3:49767000-49773600	Strong transcription	Thymus	Thymus
37	chr3:49767400-49775800	Strong transcription	Liver	Liver
38	chr3:49767400-49776400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr3:49767400-49776400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr3:49767400-49776400	Strong transcription	Primary T helper cells fromperipheralblood	blood
41	chr3:49767400-49776400	Strong transcription	Adipose Nuclei	Adipose
42	chr3:49767400-49777600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr3:49767600-49773600	Strong transcription	Brain Hippocampus Middle	brain
44	chr3:49767600-49773600	Strong transcription	Lung	lung
45	chr3:49767600-49775800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr3:49767600-49776000	Strong transcription	GM12878-XiMat	blood
47	chr3:49767600-49776400	Strong transcription	Ovary	ovary
48	chr3:49767600-49776400	Strong transcription	Osteobl	bone
49	chr3:49767600-49776600	Strong transcription	HUES64 Cell Line	embryonic stem cell
50	chr3:49767600-49776600	Strong transcription	Rectal Mucosa Donor 31	rectum

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