Variant report

Variant	rs10424841
Chromosome Location	chr19:37576550-37576551
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	chr19:37569073..37571091-chr19:37575937..37578099,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000197050	Chromatin interaction
ENSG00000267345	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10401380	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10401525	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10401561	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10402050	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10404069	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10404973	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10405372	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10406612	0.84[CEU][hapmap];1.00[CHB][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.84[EUR][1000 genomes]
rs10407014	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10407224	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10407265	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10408199	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10410594	0.85[YRI][hapmap]
rs10410905	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10411037	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10411176	0.84[CEU][hapmap];1.00[CHB][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.86[MKK][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10412236	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10413101	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10413304	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10414107	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10414227	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10414983	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10416960	0.87[YRI][hapmap]
rs10417545	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10418314	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10419174	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.94[TSI][hapmap];0.92[YRI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10419845	0.85[EUR][1000 genomes]
rs10422428	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10425441	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10426093	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11084873	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12972146	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12975706	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12978093	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12983153	0.88[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13346284	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1617883	0.93[EUR][1000 genomes]
rs1624293	0.89[CEU][hapmap]
rs1628959	0.88[EUR][1000 genomes]
rs1644702	0.89[EUR][1000 genomes]
rs1644704	0.89[EUR][1000 genomes]
rs17707101	0.87[YRI][hapmap]
rs2385412	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28462002	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28631881	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28660259	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28701616	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34193103	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34915391	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35522655	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35655645	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3816391	0.87[YRI][hapmap]
rs4473303	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4805198	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4805207	0.84[CEU][hapmap];0.88[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.86[MKK][hapmap];0.83[TSI][hapmap];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4805208	0.84[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.83[TSI][hapmap];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4806380	0.87[YRI][hapmap]
rs4806406	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4806414	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.94[TSI][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62108899	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62109879	0.93[EUR][1000 genomes]
rs6510583	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7246473	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7247758	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7249696	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7259878	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8101338	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8111936	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1064851	chr19:36910259-37689721	Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv1065698	chr19:36916796-37690124	Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv543999	chr19:36916796-37690124	Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv529817	chr19:36930549-37654062	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
5	nsv918028	chr19:37020645-38014526	Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
6	esv3507199	chr19:37284708-37805639	Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
7	esv3507200	chr19:37284708-37805639	ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
8	esv3497360	chr19:37290273-37745365	ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
9	esv3497361	chr19:37290273-37745365	Active TSS ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers 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	25 gene(s)	inside rSNPs	diseases
10	nsv458568	chr19:37325826-37747108	Strong transcription ZNF genes & repeats Genic enhancers Active TSS Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
11	nsv579461	chr19:37325826-37747108	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
12	nsv833818	chr19:37427808-37602800	Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
13	nsv911652	chr19:37437106-37774299	Weak transcription ZNF genes & repeats Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers 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	17 gene(s)	inside rSNPs	diseases
14	nsv911654	chr19:37487632-37758082	Strong transcription Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs10424841	AXL	cis	cerebellum	SCAN
rs10424841	CEACAM16	cis	cerebellum	SCAN
rs10424841	SERTAD3	cis	parietal	SCAN
rs10424841	EXOSC5	cis	cerebellum	SCAN
rs10424841	ZNF420	cis	lymphoblastoid	seeQTL
rs10424841	ITPKC	cis	cerebellum	SCAN
rs10424841	MEGF8	cis	cerebellum	SCAN
rs10424841	PAFAH1B3	cis	cerebellum	SCAN
rs10424841	VASP	cis	parietal	SCAN
rs10424841	SNRPD2	cis	parietal	SCAN
rs10424841	ZNF420	cis	Liver	GTEx
rs10424841	ZNF420	cis	multi-tissue	Pritchard
rs10424841	XRCC1	cis	parietal	SCAN

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:37570600-37580000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr19:37570600-37581000	Weak transcription	Gastric	stomach
3	chr19:37570600-37581600	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr19:37570800-37579800	Weak transcription	Hela-S3	cervix
5	chr19:37571000-37580000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr19:37571000-37594800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr19:37571200-37577800	Weak transcription	Right Ventricle	heart
8	chr19:37571400-37578000	ZNF genes & repeats	Dnd41	blood
9	chr19:37572400-37578200	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
10	chr19:37572400-37594600	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
11	chr19:37572600-37595400	ZNF genes & repeats	Adipose Nuclei	Adipose
12	chr19:37572800-37577800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr19:37572800-37578000	ZNF genes & repeats	Brain Hippocampus Middle	brain
14	chr19:37572800-37594600	ZNF genes & repeats	Primary hematopoietic stem cells	blood
15	chr19:37572800-37594800	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
16	chr19:37572800-37595400	ZNF genes & repeats	Liver	Liver
17	chr19:37573400-37577800	ZNF genes & repeats	Brain Substantia Nigra	brain
18	chr19:37573800-37577000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr19:37574400-37577000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr19:37574600-37579600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr19:37575400-37576600	ZNF genes & repeats	Brain Anterior Caudate	brain
22	chr19:37575400-37580000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr19:37575400-37592400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr19:37575400-37595200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr19:37575800-37576600	ZNF genes & repeats	Primary T cells fromperipheralblood	blood
26	chr19:37575800-37576600	ZNF genes & repeats	Primary T killer naive cells fromperipheralblood	blood
27	chr19:37575800-37577200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr19:37575800-37578000	ZNF genes & repeats	Primary T helper memory cells from peripheral blood 1	blood
29	chr19:37575800-37594800	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
30	chr19:37576000-37576600	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr19:37576000-37576600	ZNF genes & repeats	Brain Cingulate Gyrus	brain
32	chr19:37576000-37577400	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
33	chr19:37576000-37577600	ZNF genes & repeats	Brain Germinal Matrix	brain
34	chr19:37576000-37577600	ZNF genes & repeats	Colon Smooth Muscle	Colon
35	chr19:37576000-37577800	ZNF genes & repeats	Fetal Brain Female	brain
36	chr19:37576000-37578000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr19:37576000-37578000	ZNF genes & repeats	Rectal Smooth Muscle	rectum
38	chr19:37576000-37578200	ZNF genes & repeats	Primary B cells from peripheral blood	blood
39	chr19:37576000-37578200	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr19:37576000-37578200	ZNF genes & repeats	Fetal Lung	lung
41	chr19:37576000-37578200	ZNF genes & repeats	Skeletal Muscle Female	skeletal muscle
42	chr19:37576000-37578400	ZNF genes & repeats	Duodenum Mucosa	Duodenum
43	chr19:37576000-37580600	ZNF genes & repeats	Fetal Intestine Large	intestine
44	chr19:37576000-37587800	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
45	chr19:37576200-37576600	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr19:37576200-37576600	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr19:37576200-37576600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr19:37576200-37576600	ZNF genes & repeats	Brain Dorsolateral Prefrontal Cortex	brain
49	chr19:37576200-37576800	Strong transcription	Primary T helper naive cells from peripheral blood	blood
50	chr19:37576200-37577200	ZNF genes & repeats	Aorta	Aorta

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