Variant report

Variant	rs2740174
Chromosome Location	chr1:226033969-226033970
allele	A/G
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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:226032510..226034899-chr1:226069383..226071490,2	MCF-7	breast:
2	chr1:226033213..226034060-chr1:226163734..226164318,2	K562	blood:
3	chr1:226033230..226036408-chr1:226061975..226066194,3	MCF-7	breast:
4	chr1:225963673..225968224-chr1:226032543..226034938,4	MCF-7	breast:
5	chr1:225964834..225965851-chr1:226033204..226034086,4	K562	blood:
6	chr1:226032235..226034217-chr1:226150384..226152008,2	K562	blood:
7	chr1:225964257..225969087-chr1:226030786..226035881,7	K562	blood:
8	chr1:225662402..225663343-chr1:226032820..226034152,12	MCF-7	breast:
9	chr1:225963873..225967033-chr1:226031330..226035962,4	MCF-7	breast:
10	chr1:225662312..225663277-chr1:226032721..226034082,11	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000196187	Chromatin interaction
ENSG00000213032	Chromatin interaction
ENSG00000143742	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs1051741	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.88[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.86[TSI][hapmap];0.91[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2234922	0.82[CHB][hapmap];0.92[CHD][hapmap]
rs2292558	0.91[CEU][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2671264	0.82[CHB][hapmap];0.92[CHD][hapmap]
rs2671266	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2671267	0.82[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56108141	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1795046	chr1:225874059-226091150	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	esv1834932	chr1:225874059-226091150	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	esv1834948	chr1:225874059-226214882	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
4	nsv524126	chr1:225973777-226210653	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
5	nsv947519	chr1:225998770-226034631	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv873231	chr1:226019653-226134471	Enhancers Transcr. at gene 5' and 3' Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
7	esv2762223	chr1:226025175-226201716	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
8	nsv520628	chr1:226026406-226093362	Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
9	esv1801609	chr1:226027323-226036309	Weak transcription Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	esv1802694	chr1:226032229-226036309	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2740174	MIA3	cis	cerebellum	SCAN
rs2740174	ZNF678	cis	parietal	SCAN
rs2740174	LEFTY2	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:226013600-226052600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:226013800-226037200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr1:226014600-226035600	Weak transcription	Small Intestine	intestine
4	chr1:226014800-226047800	Weak transcription	Psoas Muscle	Psoas
5	chr1:226016000-226051000	Weak transcription	NH-A	brain
6	chr1:226017400-226049800	Weak transcription	HUVEC	blood vessel
7	chr1:226020600-226042000	Weak transcription	Hela-S3	cervix
8	chr1:226020600-226042400	Weak transcription	HSMM	muscle
9	chr1:226023000-226039600	Weak transcription	NHDF-Ad	bronchial
10	chr1:226023800-226035800	Weak transcription	Fetal Brain Male	brain
11	chr1:226024600-226034000	Weak transcription	Primary hematopoietic stem cells	blood
12	chr1:226025800-226034800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr1:226025800-226036400	Strong transcription	Lung	lung
14	chr1:226025800-226036400	Strong transcription	Osteobl	bone
15	chr1:226026000-226034200	Strong transcription	Ovary	ovary
16	chr1:226026200-226035200	Strong transcription	Rectal Mucosa Donor 29	rectum
17	chr1:226026800-226061600	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr1:226029600-226035600	Genic enhancers	Brain Hippocampus Middle	brain
19	chr1:226029800-226035000	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr1:226029800-226035200	Strong transcription	Fetal Brain Female	brain
21	chr1:226029800-226035400	Strong transcription	Spleen	Spleen
22	chr1:226029800-226037600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr1:226029800-226050600	Strong transcription	Right Ventricle	heart
24	chr1:226030000-226040200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr1:226030200-226034000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr1:226030200-226034200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr1:226030200-226039000	Genic enhancers	Brain Substantia Nigra	brain
28	chr1:226030400-226034000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr1:226030400-226034800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr1:226030400-226036000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr1:226030400-226046800	Strong transcription	Primary neutrophils fromperipheralblood	blood
32	chr1:226030400-226052600	Weak transcription	HSMMtube	muscle
33	chr1:226030600-226039400	Strong transcription	Liver	Liver
34	chr1:226030800-226037000	Weak transcription	Right Atrium	heart
35	chr1:226030800-226037400	Strong transcription	NHLF	lung
36	chr1:226031200-226034000	Genic enhancers	Adipose Nuclei	Adipose
37	chr1:226031200-226037200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr1:226031400-226037800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr1:226031800-226036600	Strong transcription	iPS-15b Cell Line	embryonic stem cell
40	chr1:226031800-226039600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
41	chr1:226032000-226034800	Strong transcription	Rectal Mucosa Donor 31	rectum
42	chr1:226032000-226034800	Strong transcription	Sigmoid Colon	Sigmoid Colon
43	chr1:226032000-226036200	Genic enhancers	Brain Angular Gyrus	brain
44	chr1:226032000-226037400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr1:226032000-226037800	Strong transcription	Aorta	Aorta
46	chr1:226032200-226036800	Strong transcription	Brain Germinal Matrix	brain
47	chr1:226032400-226036600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr1:226032400-226039000	Genic enhancers	Fetal Muscle Trunk	muscle
49	chr1:226032600-226034000	Enhancers	H1 Cell Line	embryonic stem cell
50	chr1:226032600-226034000	Genic enhancers	Fetal Lung	lung

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