Variant report

Variant	rs10411640
Chromosome Location	chr19:56105161-56105162
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:56103233..56104833-chr19:56105149..56107018,2	MCF-7	breast:
2	chr19:56098773..56102057-chr19:56102785..56106000,5	K562	blood:

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs2037240	0.93[CEU][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4801603	1.00[JPT][hapmap]
rs7507151	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv912473	chr19:55874642-56145428	Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases
2	nsv912486	chr19:55977909-56145428	Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
3	nsv912487	chr19:55977909-56215184	Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
4	nsv912494	chr19:56026072-56215184	Genic enhancers Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
5	nsv912495	chr19:56033088-56132661	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
6	nsv912496	chr19:56040051-56145428	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
7	nsv912497	chr19:56041848-56145428	Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic 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 target site	55 gene(s)	inside rSNPs	diseases
8	nsv912498	chr19:56041848-56215184	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
9	nsv828643	chr19:56059280-56154823	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer 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	67 gene(s)	inside rSNPs	diseases
10	nsv912499	chr19:56071293-56132487	Flanking Active TSS Genic enhancers Active TSS Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
11	nsv912500	chr19:56078722-56175515	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	86 gene(s)	inside rSNPs	diseases
12	nsv912501	chr19:56093365-56215184	Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
13	nsv912502	chr19:56099884-56138575	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
14	esv3436946	chr19:56102240-56106638	Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
15	esv3419513	chr19:56103040-56105838	Strong transcription Weak transcription Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats	Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases
16	esv3357075	chr19:56103490-56105838	Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
17	esv3356414	chr19:56103565-56106113	Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10411640	ZNF460	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56097800-56106600	Weak transcription	Aorta	Aorta
2	chr19:56098800-56106200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr19:56098800-56106200	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr19:56098800-56106200	Weak transcription	Small Intestine	intestine
5	chr19:56098800-56106400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr19:56098800-56106600	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr19:56098800-56106600	Weak transcription	HSMMtube	muscle
8	chr19:56098800-56109800	Weak transcription	Fetal Heart	heart
9	chr19:56099000-56105800	Weak transcription	HSMM	muscle
10	chr19:56099000-56106200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr19:56099000-56106200	Weak transcription	Psoas Muscle	Psoas
12	chr19:56099000-56106200	Weak transcription	Rectal Smooth Muscle	rectum
13	chr19:56099000-56106800	Weak transcription	Colon Smooth Muscle	Colon
14	chr19:56099000-56106800	Weak transcription	NHDF-Ad	bronchial
15	chr19:56099000-56107000	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr19:56099200-56106200	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr19:56099200-56106200	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr19:56099200-56106200	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr19:56099200-56106200	Weak transcription	GM12878-XiMat	blood
20	chr19:56099200-56106200	Weak transcription	Hela-S3	cervix
21	chr19:56099200-56106200	Weak transcription	Osteobl	bone
22	chr19:56099200-56106400	Weak transcription	Fetal Brain Male	brain
23	chr19:56099200-56106400	Weak transcription	Fetal Kidney	kidney
24	chr19:56099200-56106400	Weak transcription	HepG2	liver
25	chr19:56099200-56106400	Weak transcription	HUVEC	blood vessel
26	chr19:56099200-56107000	Weak transcription	HMEC	breast
27	chr19:56099200-56110000	Weak transcription	Right Atrium	heart
28	chr19:56099400-56106000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr19:56099400-56106400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr19:56099600-56106200	Weak transcription	Primary hematopoietic stem cells	blood
31	chr19:56099800-56106200	Weak transcription	Primary B cells from cord blood	blood
32	chr19:56099800-56106200	Weak transcription	Primary T helper cells PMA-I stimulated	--
33	chr19:56099800-56110000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr19:56099800-56110400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr19:56100000-56106400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
36	chr19:56100000-56109800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr19:56102000-56106200	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr19:56102000-56109800	Strong transcription	Fetal Stomach	stomach
39	chr19:56102600-56106600	Strong transcription	Brain Germinal Matrix	brain
40	chr19:56102600-56109200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
41	chr19:56102600-56109200	Strong transcription	Fetal Brain Female	brain
42	chr19:56102600-56109200	Strong transcription	Fetal Thymus	thymus
43	chr19:56102600-56109800	Strong transcription	Fetal Intestine Small	intestine
44	chr19:56102800-56106400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr19:56102800-56106600	Strong transcription	Fetal Muscle Leg	muscle
46	chr19:56102800-56106600	Strong transcription	Skeletal Muscle Female	skeletal muscle
47	chr19:56102800-56107200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr19:56102800-56107800	Strong transcription	Placenta Amnion	Placenta Amnion
49	chr19:56102800-56108600	Strong transcription	Brain Inferior Temporal Lobe	brain
50	chr19:56102800-56108600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain

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