Variant report

Variant	rs10407941
Chromosome Location	chr19:53288136-53288137
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs10407762	1.00[CEU][hapmap];1.00[GIH][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10416542	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10416670	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:30 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1057296	chr19:52950339-53396986	Weak transcription Active TSS ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv912305	chr19:53092465-53349850	Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv912306	chr19:53092465-53400760	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Genic enhancers Active TSS 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	31 gene(s)	inside rSNPs	diseases
4	nsv912307	chr19:53092465-53433054	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription 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	32 gene(s)	inside rSNPs	diseases
5	nsv912308	chr19:53092465-53436337	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
6	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
7	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
8	nsv912312	chr19:53103875-53296371	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
9	nsv912313	chr19:53103875-53436337	ZNF genes & repeats Weak transcription Strong transcription Active TSS 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	30 gene(s)	inside rSNPs	diseases
10	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
11	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
12	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
13	esv3489404	chr19:53121944-53391394	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
14	esv3489405	chr19:53121944-53391394	Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
15	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
16	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
17	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
18	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
19	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
20	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
21	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
22	nsv1067557	chr19:53195426-53319092	Enhancers Active TSS ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
23	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
24	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
25	nsv833875	chr19:53211335-53391459	Enhancers Strong transcription Active TSS Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer 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	19 gene(s)	inside rSNPs	diseases
26	nsv961240	chr19:53242965-53395960	Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
27	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
28	nsv1066277	chr19:53261575-53364138	ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
29	nsv1061781	chr19:53263785-53364138	Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
30	nsv1061149	chr19:53266861-53364138	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs10407941	TTYH1	cis	parietal	SCAN
rs10407941	SSC5D	cis	cerebellum	SCAN
rs10407941	LAIR2	cis	parietal	SCAN
rs10407941	U2AF2	cis	cerebellum	SCAN
rs10407941	LENG9	cis	cerebellum	SCAN
rs10407941	HOXC12	trans	parietal	SCAN

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:53270400-53288800	Weak transcription	Osteobl	bone
2	chr19:53270400-53289000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr19:53270400-53289200	Weak transcription	NHLF	lung
4	chr19:53270400-53289400	Weak transcription	Brain Anterior Caudate	brain
5	chr19:53270600-53289200	Weak transcription	Brain Substantia Nigra	brain
6	chr19:53270800-53289400	Weak transcription	Fetal Muscle Trunk	muscle
7	chr19:53271200-53289200	Weak transcription	Brain Hippocampus Middle	brain
8	chr19:53271600-53289000	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr19:53273600-53288600	Weak transcription	K562	blood
10	chr19:53273600-53289400	Weak transcription	Colon Smooth Muscle	Colon
11	chr19:53273800-53289200	Weak transcription	Psoas Muscle	Psoas
12	chr19:53274200-53288600	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr19:53276200-53289000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr19:53276200-53289000	Weak transcription	Right Ventricle	heart
15	chr19:53277000-53289200	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr19:53277000-53289200	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr19:53277600-53289000	Weak transcription	Pancreas	Pancrea
18	chr19:53277800-53289200	Weak transcription	Fetal Muscle Leg	muscle
19	chr19:53278000-53289400	Weak transcription	Small Intestine	intestine
20	chr19:53278000-53289400	Weak transcription	HSMMtube	muscle
21	chr19:53278200-53289000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr19:53278200-53289200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr19:53278400-53289000	Weak transcription	Colonic Mucosa	Colon
24	chr19:53280800-53289200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr19:53281200-53289200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr19:53282000-53288800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr19:53282000-53289000	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr19:53282000-53289200	Weak transcription	Fetal Stomach	stomach
29	chr19:53282000-53289200	Weak transcription	Left Ventricle	heart
30	chr19:53282000-53289200	Weak transcription	Ovary	ovary
31	chr19:53282200-53288800	Weak transcription	Stomach Smooth Muscle	stomach
32	chr19:53282200-53289200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr19:53282400-53288600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr19:53282400-53289000	Weak transcription	Hela-S3	cervix
35	chr19:53283400-53289400	Weak transcription	Aorta	Aorta
36	chr19:53284200-53288600	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr19:53284400-53289000	Weak transcription	Thymus	Thymus
38	chr19:53284600-53289000	Weak transcription	Rectal Smooth Muscle	rectum
39	chr19:53284600-53289000	Weak transcription	NHEK	skin
40	chr19:53284600-53289200	Weak transcription	Adipose Nuclei	Adipose
41	chr19:53284800-53288800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr19:53284800-53288800	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr19:53284800-53289000	Weak transcription	HMEC	breast
44	chr19:53285000-53288200	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr19:53285000-53288600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr19:53285000-53288600	Weak transcription	Primary B cells from cord blood	blood
47	chr19:53285000-53288600	Weak transcription	Spleen	Spleen
48	chr19:53285000-53288800	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr19:53285000-53289000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr19:53285000-53289000	Weak transcription	Duodenum Smooth Muscle	Duodenum

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