Variant report

Variant	rs10403272
Chromosome Location	chr19:19189316-19189317
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:19028585..19031499-chr19:19189292..19192054,2	K562	blood:
2	chr19:19174780..19177149-chr19:19188353..19191125,2	K562	blood:
3	chr19:19187798..19189522-chr19:19193130..19195323,2	K562	blood:
4	chr19:19187730..19190152-chr19:19246123..19249004,2	K562	blood:

Variant related genes	Relation type
ENSG00000105671	Chromatin interaction
ENSG00000181035	Chromatin interaction
ENSG00000105669	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10410399	1.00[ASW][hapmap];0.92[CEU][hapmap];0.96[GIH][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11085249	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11671696	0.89[ASN][1000 genomes]
rs2013813	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2269807	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2269869	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs3787041	0.85[JPT][hapmap]
rs4808172	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs4808176	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs4808177	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4808182	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4808895	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4808900	0.89[ASN][1000 genomes]
rs4808916	0.83[CEU][hapmap];0.85[JPT][hapmap]
rs4808917	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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6511019	1.00[ASW][hapmap];0.83[CEU][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap]
rs7252615	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs757222	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833778	chr19:19012669-19201487	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
2	nsv1059305	chr19:19131310-19209999	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	21 gene(s)	inside rSNPs	diseases
3	nsv833779	chr19:19163492-19313091	Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10403272	SFRS14	Cis_1M	lymphoblastoid	RTeQTL
rs10403272	KIAA1683	cis	cerebellum	SCAN
rs10403272	ZNF14	cis	parietal	SCAN

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19175400-19207800	Weak transcription	Aorta	Aorta
2	chr19:19176400-19190400	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr19:19176400-19190600	Weak transcription	Esophagus	oesophagus
4	chr19:19176400-19192600	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr19:19176400-19192600	Weak transcription	Right Atrium	heart
6	chr19:19176400-19215200	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr19:19176400-19215800	Weak transcription	Rectal Smooth Muscle	rectum
8	chr19:19176400-19215800	Weak transcription	NHLF	lung
9	chr19:19176600-19190200	Weak transcription	Fetal Kidney	kidney
10	chr19:19176600-19194400	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr19:19176600-19206800	Weak transcription	Fetal Brain Female	brain
12	chr19:19176600-19207200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr19:19176600-19208200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr19:19177000-19210000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr19:19177200-19204800	Weak transcription	Fetal Intestine Large	intestine
16	chr19:19177200-19215400	Weak transcription	Colonic Mucosa	Colon
17	chr19:19178400-19204800	Weak transcription	HepG2	liver
18	chr19:19178600-19198400	Weak transcription	Brain Substantia Nigra	brain
19	chr19:19180200-19216000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr19:19180400-19189400	Strong transcription	Fetal Stomach	stomach
21	chr19:19180400-19192200	Weak transcription	Placenta	Placenta
22	chr19:19180400-19192400	Weak transcription	Adipose Nuclei	Adipose
23	chr19:19180400-19192400	Weak transcription	Left Ventricle	heart
24	chr19:19180400-19194600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr19:19180400-19195800	Weak transcription	Brain Cingulate Gyrus	brain
26	chr19:19180400-19207200	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr19:19180400-19207800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr19:19180400-19208000	Weak transcription	Brain Angular Gyrus	brain
29	chr19:19180400-19208000	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr19:19180400-19208200	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr19:19180400-19216400	Weak transcription	Colon Smooth Muscle	Colon
32	chr19:19180400-19219800	Weak transcription	HSMMtube	muscle
33	chr19:19180600-19208200	Weak transcription	Fetal Lung	lung
34	chr19:19180600-19213600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr19:19180600-19245600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
36	chr19:19180600-19248400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr19:19183800-19189400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr19:19184000-19190600	Strong transcription	Primary T cells from cord blood	blood
39	chr19:19184000-19190600	Weak transcription	Gastric	stomach
40	chr19:19185400-19190000	Strong transcription	Primary B cells from peripheral blood	blood
41	chr19:19185400-19190800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr19:19185400-19192200	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr19:19185400-19194800	Strong transcription	Stomach Smooth Muscle	stomach
44	chr19:19185400-19208400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
45	chr19:19185400-19221200	Weak transcription	Primary hematopoietic stem cells	blood
46	chr19:19185600-19189600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr19:19185600-19190600	Weak transcription	Lung	lung
48	chr19:19185600-19192000	Weak transcription	Fetal Brain Male	brain
49	chr19:19185600-19192400	Weak transcription	Psoas Muscle	Psoas
50	chr19:19185600-19194400	Weak transcription	Brain Germinal Matrix	brain

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