Variant report

Variant	rs10402901
Chromosome Location	chr19:53440375-53440376
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:53437779..53441076-chr19:53444311..53446958,6	K562	blood:
2	chr19:53399445..53402130-chr19:53440139..53442366,2	K562	blood:
3	chr19:53438104..53442400-chr19:53444179..53446884,10	K562	blood:
4	chr19:53425069..53426727-chr19:53438910..53441039,3	K562	blood:
5	chr19:53399145..53401987-chr19:53438300..53441406,3	K562	blood:

Variant related genes	Relation type
ENSG00000182986	Chromatin interaction
ENSG00000180257	Chromatin interaction
ENSG00000269646	Chromatin interaction
ENSG00000213793	Chromatin interaction
ENSG00000213801	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10402011	0.85[YRI][hapmap]
rs10406237	1.00[CHB][hapmap]
rs10408553	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10410030	1.00[CHB][hapmap]
rs11084197	1.00[CHB][hapmap]
rs11668258	1.00[CHB][hapmap]
rs12971916	1.00[CHB][hapmap]
rs12982323	1.00[CHB][hapmap]
rs1661923	1.00[CHB][hapmap]
rs16984438	1.00[CHB][hapmap]
rs16984443	1.00[CHB][hapmap]
rs16984486	1.00[CHB][hapmap]
rs17770717	1.00[JPT][hapmap];0.84[MEX][hapmap]
rs6509725	1.00[CHB][hapmap]
rs7247568	1.00[CHB][hapmap]
rs8102799	1.00[CHB][hapmap]
rs8109900	1.00[CHB][hapmap]
rs8110394	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:26 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv912309	chr19:53092465-53440653	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS 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	32 gene(s)	inside rSNPs	diseases
2	nsv912310	chr19:53092465-53451291	Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv912317	chr19:53105547-53440653	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	nsv1066762	chr19:53112568-53552217	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
5	nsv912318	chr19:53118278-53451291	Strong transcription ZNF genes & repeats Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv432072	chr19:53144788-53554388	Strong transcription ZNF genes & repeats Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
7	esv3401212	chr19:53151131-53482063	Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
8	nsv912321	chr19:53186836-53451291	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
9	nsv1058903	chr19:53193570-53489633	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
10	nsv1067280	chr19:53193570-53567287	Active TSS Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
11	nsv544062	chr19:53193570-53567287	ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer 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	33 gene(s)	inside rSNPs	diseases
12	nsv580030	chr19:53194344-53547394	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
13	nsv1057118	chr19:53195426-53480449	Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
14	nsv530807	chr19:53210488-53695881	Strong transcription Active TSS Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS 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 target site	43 gene(s)	inside rSNPs	diseases
15	nsv912323	chr19:53249347-53451291	ZNF genes & repeats Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription 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	20 gene(s)	inside rSNPs	diseases
16	esv3431689	chr19:53291230-53483998	Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
17	nsv912329	chr19:53317001-53440653	Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
18	nsv912330	chr19:53317001-53478109	Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Enhancers 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 target site	18 gene(s)	inside rSNPs	diseases
19	nsv1064234	chr19:53346827-53480449	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
20	esv3319159	chr19:53361167-53446431	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
21	esv3319160	chr19:53361308-53446343	ZNF genes & repeats Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
22	esv3326632	chr19:53371248-53697569	Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
23	nsv963071	chr19:53401720-53480869	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
24	esv2758506	chr19:53410459-53652575	ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
25	esv2758769	chr19:53410459-53652575	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
26	nsv428370	chr19:53410459-53652575	Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10402901	TRIM28	cis	parietal	SCAN
rs10402901	ZNF581	cis	cerebellum	SCAN

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:53426600-53444800	Weak transcription	Fetal Heart	heart
2	chr19:53426800-53444800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr19:53426800-53445000	Weak transcription	Small Intestine	intestine
4	chr19:53426800-53445200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr19:53426800-53445200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr19:53427000-53442600	Weak transcription	Ovary	ovary
7	chr19:53427000-53444800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr19:53427400-53444800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr19:53427400-53445000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr19:53427400-53445200	Weak transcription	Left Ventricle	heart
11	chr19:53427600-53442200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr19:53427600-53444600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr19:53427600-53444800	Weak transcription	NHDF-Ad	bronchial
14	chr19:53427800-53444800	Weak transcription	Rectal Smooth Muscle	rectum
15	chr19:53427800-53445200	Weak transcription	NHLF	lung
16	chr19:53428400-53440400	Weak transcription	NHEK	skin
17	chr19:53428600-53444800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr19:53432000-53444600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr19:53432000-53444800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr19:53432200-53442200	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr19:53432400-53440800	Weak transcription	Dnd41	blood
22	chr19:53432400-53444800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr19:53432400-53444800	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr19:53432600-53440400	Weak transcription	HSMM	muscle
25	chr19:53432600-53441600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr19:53432600-53442600	Weak transcription	Primary neutrophils fromperipheralblood	blood
27	chr19:53432600-53444800	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr19:53432600-53444800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr19:53432600-53445000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr19:53432600-53445000	Weak transcription	Fetal Muscle Leg	muscle
31	chr19:53432600-53445000	Weak transcription	HSMMtube	muscle
32	chr19:53433000-53444600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr19:53433600-53444800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr19:53434000-53442800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr19:53435400-53441000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr19:53435400-53441000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr19:53435600-53441400	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr19:53437600-53440600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr19:53437800-53440400	Enhancers	Primary hematopoietic stem cells	blood
40	chr19:53437800-53441200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr19:53438000-53440400	Enhancers	Placenta Amnion	Placenta Amnion
42	chr19:53438000-53441200	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr19:53438200-53443200	Enhancers	Stomach Mucosa	stomach
44	chr19:53438400-53444600	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr19:53438400-53444800	Weak transcription	Right Ventricle	heart
46	chr19:53438600-53440400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr19:53438800-53441400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr19:53438800-53444600	Enhancers	Placenta	Placenta
49	chr19:53439000-53441200	Strong transcription	Duodenum Mucosa	Duodenum
50	chr19:53439000-53444800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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