Variant report

Variant	rs12250140
Chromosome Location	chr10:43898776-43898777
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:43897221..43899956-chr10:43931853..43934040,2	MCF-7	breast:
2	chr10:43753888..43756103-chr10:43898148..43900430,2	K562	blood:
3	chr10:43857152..43860399-chr10:43897567..43900656,3	MCF-7	breast:
4	chr10:43853717..43856256-chr10:43898342..43901234,2	MCF-7	breast:
5	chr10:43887055..43906178-chr10:43946385..43955803,85	K562	blood:

Variant related genes	Relation type
ENSG00000252532	Chromatin interaction
ENSG00000243660	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10409	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10466239	0.86[ASN][1000 genomes]
rs10899791	0.92[ASN][1000 genomes]
rs10899793	0.92[ASN][1000 genomes]
rs10899794	0.90[JPT][hapmap]
rs10899796	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10899797	0.90[JPT][hapmap]
rs10899800	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10899801	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10899802	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10899803	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10899806	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10899807	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10899808	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11238525	0.90[ASN][1000 genomes]
rs11238530	0.96[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs11238532	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11238536	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11238553	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11238558	0.96[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs11238572	0.81[AMR][1000 genomes]
rs11525297	0.92[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11814409	0.85[CHB][hapmap]
rs11815101	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12220230	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12220528	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12245541	0.84[ASN][1000 genomes]
rs12254798	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12261855	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12262836	0.81[AMR][1000 genomes]
rs13376803	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13376924	0.88[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs17153534	0.92[ASN][1000 genomes]
rs2247979	0.90[JPT][hapmap]
rs2247981	0.90[JPT][hapmap]
rs2250444	0.90[JPT][hapmap]
rs2252783	0.80[JPT][hapmap]
rs2261636	0.90[JPT][hapmap]
rs28865415	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4648316	0.92[ASN][1000 genomes]
rs4948726	0.90[JPT][hapmap]
rs56198445	0.86[ASN][1000 genomes]
rs59383062	0.92[ASN][1000 genomes]
rs6593513	0.81[JPT][hapmap]
rs7099802	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7905676	0.90[JPT][hapmap]
rs7907179	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7921001	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430159	chr10:43291894-43946294	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
2	nsv895087	chr10:43783339-43982390	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
3	nsv831842	chr10:43846541-43987501	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
4	nsv895088	chr10:43871999-44003101	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
5	nsv825354	chr10:43883418-43949936	Flanking Active TSS Active TSS Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
6	nsv825355	chr10:43890579-43923802	Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised 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	55 gene(s)	inside rSNPs	diseases
7	nsv825356	chr10:43893080-43946515	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	63 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12250140	HNRPF	cis	multi-tissue	Pritchard

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:43893200-43901600	Weak transcription	HSMMtube	muscle
2	chr10:43893400-43899800	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
3	chr10:43893400-43901400	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr10:43893600-43899000	Enhancers	HUVEC	blood vessel
5	chr10:43893600-43899800	Genic enhancers	NHEK	skin
6	chr10:43893600-43901200	Weak transcription	Brain Angular Gyrus	brain
7	chr10:43893600-43902200	Weak transcription	Aorta	Aorta
8	chr10:43893800-43898800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr10:43893800-43899000	Weak transcription	Brain Substantia Nigra	brain
10	chr10:43894000-43899400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr10:43894000-43899800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr10:43894000-43901200	Weak transcription	Brain Hippocampus Middle	brain
13	chr10:43894000-43901200	Genic enhancers	Fetal Intestine Small	intestine
14	chr10:43894000-43901400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr10:43894200-43899200	Genic enhancers	Primary T cells fromperipheralblood	blood
16	chr10:43894200-43899200	Transcr. at gene 5' and 3'	K562	blood
17	chr10:43894200-43901200	Weak transcription	Brain Anterior Caudate	brain
18	chr10:43894200-43901400	Weak transcription	Fetal Brain Male	brain
19	chr10:43894400-43898800	Genic enhancers	HMEC	breast
20	chr10:43894400-43899800	Genic enhancers	Primary B cells from peripheral blood	blood
21	chr10:43894400-43900200	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
22	chr10:43894400-43901200	Enhancers	ES-I3 Cell Line	embryonic stem cell
23	chr10:43894400-43901200	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr10:43894400-43901600	Weak transcription	Brain Germinal Matrix	brain
25	chr10:43894800-43899800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
26	chr10:43894800-43899800	Genic enhancers	Monocytes-CD14+_RO01746	blood
27	chr10:43894800-43901400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
28	chr10:43894800-43901600	Weak transcription	Fetal Brain Female	brain
29	chr10:43895000-43899000	Genic enhancers	NHDF-Ad	bronchial
30	chr10:43895000-43899200	Weak transcription	Lung	lung
31	chr10:43895000-43899400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
32	chr10:43895000-43899400	Weak transcription	Right Ventricle	heart
33	chr10:43895000-43900000	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr10:43895000-43901200	Weak transcription	Brain Cingulate Gyrus	brain
35	chr10:43895000-43901200	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr10:43895200-43899200	Weak transcription	Rectal Smooth Muscle	rectum
37	chr10:43895200-43899400	Strong transcription	HSMM	muscle
38	chr10:43895200-43901200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr10:43895200-43901600	Weak transcription	Fetal Kidney	kidney
40	chr10:43895400-43899200	Enhancers	Primary T cells from cord blood	blood
41	chr10:43895400-43899200	Genic enhancers	A549	lung
42	chr10:43895400-43900000	Weak transcription	Fetal Lung	lung
43	chr10:43895400-43900400	Weak transcription	Stomach Smooth Muscle	stomach
44	chr10:43895600-43899000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr10:43895600-43899800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
46	chr10:43895600-43899800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr10:43895600-43900400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr10:43895600-43900800	Weak transcription	Fetal Muscle Trunk	muscle
49	chr10:43896200-43899400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
50	chr10:43896600-43899200	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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