Variant report

Variant	rs11124646
Chromosome Location	chr2:38954419-38954420
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:38829435..38831561-chr2:38952602..38955088,2	MCF-7	breast:
2	chr2:38824669..38828895-chr2:38950792..38955552,5	K562	blood:
3	chr2:38952964..38955147-chr2:38962662..38964178,2	K562	blood:
4	chr2:38951822..38954678-chr2:38974984..38978674,3	MCF-7	breast:
5	chr2:38803779..38806486-chr2:38953077..38954678,2	MCF-7	breast:
6	chr2:38948167..38950183-chr2:38951156..38954719,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000235586	Chromatin interaction
ENSG00000115875	Chromatin interaction
ENSG00000143889	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10173118	0.94[CHB][hapmap];0.86[CHD][hapmap]
rs10173240	0.86[CHB][hapmap]
rs10176932	0.88[CHB][hapmap]
rs11124645	0.86[ASN][1000 genomes]
rs1138974	0.92[ASN][1000 genomes]
rs11694383	0.94[CHB][hapmap];0.90[JPT][hapmap]
rs12474770	0.84[EUR][1000 genomes]
rs12621103	0.92[CEU][hapmap];0.90[TSI][hapmap];0.84[EUR][1000 genomes]
rs12712614	0.87[ASN][1000 genomes]
rs12712621	0.86[CHB][hapmap]
rs13011311	0.97[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs13024811	0.92[CEU][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes]
rs13029406	0.88[CHB][hapmap];0.83[CHD][hapmap]
rs13383541	0.88[CHB][hapmap]
rs1530852	0.88[CHB][hapmap];0.83[CHD][hapmap]
rs1530853	0.88[CHB][hapmap];0.83[CHD][hapmap]
rs1979142	0.88[CHB][hapmap]
rs1979143	0.88[CEU][hapmap]
rs1997377	0.94[ASW][hapmap];0.94[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap];0.93[LWK][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs2272445	1.00[ASW][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2373473	1.00[JPT][hapmap]
rs3097713	0.82[CEU][hapmap];0.81[MEX][hapmap]
rs3097714	0.88[CEU][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3097716	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3099940	1.00[JPT][hapmap]
rs3099941	1.00[JPT][hapmap]
rs3099943	0.90[JPT][hapmap]
rs3099945	0.90[JPT][hapmap]
rs3099968	0.88[CEU][hapmap]
rs3108666	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3112152	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3112156	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3112161	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3112178	0.83[CEU][hapmap];0.81[EUR][1000 genomes]
rs3112183	0.92[CEU][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes]
rs3112184	0.84[CEU][hapmap]
rs3112188	0.84[CEU][hapmap]
rs3112189	0.84[CEU][hapmap]
rs3112191	0.84[CEU][hapmap]
rs3112192	0.84[CEU][hapmap]
rs3112200	0.94[CHB][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap]
rs3112215	0.96[CEU][hapmap];0.81[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap]
rs3134628	0.84[CEU][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes]
rs3134629	0.84[EUR][1000 genomes]
rs3134630	0.84[EUR][1000 genomes]
rs35387882	0.83[EUR][1000 genomes]
rs3770681	0.88[CHB][hapmap]
rs4602206	0.94[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs4630748	0.89[CHB][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs4670891	0.93[ASN][1000 genomes]
rs4670892	0.84[EUR][1000 genomes]
rs6544173	0.94[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs6728394	1.00[CHB][hapmap];0.96[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs6731386	0.97[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6736004	0.97[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs6756847	1.00[ASW][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs7419616	0.88[CHB][hapmap];0.83[CHD][hapmap]
rs7419838	0.88[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap]
rs7581263	0.97[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7581653	0.94[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7589162	0.88[CHB][hapmap]
rs7596239	0.97[ASN][1000 genomes]
rs7603676	0.94[ASW][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[MKK][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7603821	0.96[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7604054	0.95[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs7604132	0.97[AFR][1000 genomes];0.90[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	nsv916059	chr2:38332341-39119398	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	143 gene(s)	inside rSNPs	diseases
2	nsv9646	chr2:38358311-39082189	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	141 gene(s)	inside rSNPs	diseases
3	esv1797820	chr2:38941956-38972456	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv820974	chr2:38945458-38972971	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region miRNA target site	11 gene(s)	inside rSNPs	diseases
5	esv1814150	chr2:38948483-38972456	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region miRNA target site	11 gene(s)	inside rSNPs	diseases
6	esv1795154	chr2:38951608-38971432	Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS	Chromatin interactive region miRNA target site	11 gene(s)	inside rSNPs	diseases
7	esv1800732	chr2:38951608-38973837	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	12 gene(s)	inside rSNPs	diseases
8	nsv828986	chr2:38952948-38954514	Weak transcription Enhancers Strong transcription	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
9	esv1791751	chr2:38953669-38968842	Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
10	esv2763640	chr2:38954419-38977371	Genic enhancers Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11124646	DHX57	cis	multi-tissue	Pritchard
rs11124646	DHX57	cis	cerebellum	SCAN
rs11124646	MORN2	cis	cerebellum	SCAN

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:38894400-38960600	Weak transcription	Brain Substantia Nigra	brain
2	chr2:38909400-38960600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr2:38918600-38956800	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr2:38927600-38957000	Weak transcription	Brain Hippocampus Middle	brain
5	chr2:38928800-38971600	Weak transcription	Small Intestine	intestine
6	chr2:38930000-38956600	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr2:38930600-38965000	Weak transcription	Gastric	stomach
8	chr2:38932800-38956800	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr2:38936400-38957200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr2:38936400-38960600	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr2:38936400-38968400	Weak transcription	Colonic Mucosa	Colon
12	chr2:38937200-38956600	Weak transcription	Fetal Brain Female	brain
13	chr2:38937600-38970400	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr2:38939000-38956600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr2:38939200-38958600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr2:38943600-38956000	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr2:38943600-38958600	Weak transcription	Aorta	Aorta
18	chr2:38946400-38957000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr2:38948000-38955800	Weak transcription	Fetal Intestine Large	intestine
20	chr2:38948000-38958600	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr2:38948200-38956600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr2:38948200-38956600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr2:38948200-38956600	Weak transcription	Rectal Smooth Muscle	rectum
24	chr2:38948200-38957000	Weak transcription	Spleen	Spleen
25	chr2:38948200-38958600	Weak transcription	Esophagus	oesophagus
26	chr2:38948200-38968200	Weak transcription	Stomach Mucosa	stomach
27	chr2:38948400-38956600	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr2:38948400-38958600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr2:38948400-38958800	Weak transcription	Colon Smooth Muscle	Colon
30	chr2:38948400-38964400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr2:38948400-38964600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr2:38948400-38970600	Weak transcription	NHEK	skin
33	chr2:38948600-38956600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr2:38948600-38956800	Weak transcription	Brain Anterior Caudate	brain
35	chr2:38948600-38957000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr2:38948600-38959600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr2:38948600-38970200	Weak transcription	NHDF-Ad	bronchial
38	chr2:38948600-38971200	Weak transcription	Fetal Kidney	kidney
39	chr2:38948800-38956600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr2:38948800-38956600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr2:38948800-38956800	Weak transcription	Brain Cingulate Gyrus	brain
42	chr2:38948800-38957000	Weak transcription	Lung	lung
43	chr2:38948800-38960200	Weak transcription	Hela-S3	cervix
44	chr2:38948800-38960600	Weak transcription	Brain Angular Gyrus	brain
45	chr2:38948800-38964600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr2:38949000-38956800	Weak transcription	Ovary	ovary
47	chr2:38949000-38958600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr2:38949000-38965000	Weak transcription	Right Ventricle	heart
49	chr2:38949600-38956800	Weak transcription	Osteobl	bone
50	chr2:38949800-38956600	Weak transcription	Adipose Nuclei	Adipose

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