Variant report

Variant	rs17641276
Chromosome Location	chr19:39674034-39674035
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:39643019..39646132-chr19:39671022..39674035,4	MCF-7	breast:
2	chr19:39616247..39618340-chr19:39674004..39675783,3	K562	blood:
3	chr19:39660707..39662756-chr19:39672502..39674103,2	K562	blood:
4	chr19:39671387..39675690-chr19:39676720..39678693,3	K562	blood:
5	chr19:39659195..39660829-chr19:39672092..39674140,2	MCF-7	breast:
6	chr19:39643809..39645925-chr19:39673965..39675850,2	K562	blood:
7	chr19:39601627..39603917-chr19:39672984..39674642,2	MCF-7	breast:
8	chr19:39617221..39619579-chr19:39672951..39675735,2	MCF-7	breast:
9	chr19:39672896..39675810-chr19:39732374..39734924,2	K562	blood:
10	chr19:39672992..39674987-chr19:39833706..39835660,2	K562	blood:
11	chr19:39668971..39672206-chr19:39672666..39676660,4	K562	blood:
12	chr19:39663680..39665927-chr19:39672756..39674305,2	MCF-7	breast:
13	chr19:39673403..39676045-chr19:39694848..39697748,2	K562	blood:
14	chr19:39615269..39618904-chr19:39671305..39675094,5	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000179751	Chromatin interaction
ENSG00000130669	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11083508	0.84[CEU][hapmap];0.81[CHB][hapmap]
rs11667387	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11669124	0.84[CEU][hapmap];0.81[CHB][hapmap]
rs11671084	0.88[CEU][hapmap];0.87[CHB][hapmap];0.85[YRI][hapmap]
rs11672886	0.84[CEU][hapmap];0.86[CHB][hapmap];0.90[CHD][hapmap];0.81[JPT][hapmap];0.82[TSI][hapmap]
rs11673014	0.84[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap]
rs13228	0.80[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs17708461	0.81[CEU][hapmap]
rs2304090	0.84[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs2319153	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4802021	0.83[ASN][1000 genomes]
rs4803209	0.84[CEU][hapmap];0.81[CHB][hapmap]
rs71334840	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs750247	0.90[CEU][hapmap];0.83[JPT][hapmap]
rs8101281	0.84[CEU][hapmap];0.81[CHB][hapmap]
rs8101444	0.86[AFR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs874535	0.84[CEU][hapmap];0.81[CHB][hapmap]
rs879689	0.84[CEU][hapmap];0.86[CHB][hapmap];0.90[CHD][hapmap];0.81[JPT][hapmap];0.82[TSI][hapmap]
rs9676717	0.83[CHD][hapmap];0.87[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833829	chr19:39569681-39730777	Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv432048	chr19:39572060-39850060	Bivalent/Poised TSS Bivalent Enhancer Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs17641276	SPINT2	cis	lymphoblastoid	seeQTL
rs17641276	B3GNT8	cis	cerebellum	SCAN
rs17641276	PHLDB3	cis	parietal	SCAN
rs17641276	CNFN	cis	cerebellum	SCAN
rs17641276	PVRL2	cis	parietal	SCAN
rs17641276	PAK4	cis	Skin Sun Exposed Lower leg	GTEx
rs17641276	PAK4	cis	Thyroid	GTEx
rs17641276	B9D2	cis	cerebellum	SCAN
rs17641276	CRX	cis	parietal	SCAN

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39657800-39687600	Weak transcription	Right Atrium	heart
2	chr19:39661400-39684600	Weak transcription	HSMM	muscle
3	chr19:39662600-39681800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr19:39663200-39681400	Weak transcription	Fetal Kidney	kidney
5	chr19:39666000-39676600	Weak transcription	Fetal Lung	lung
6	chr19:39666000-39677000	Weak transcription	Fetal Brain Male	brain
7	chr19:39667400-39679600	Weak transcription	HSMMtube	muscle
8	chr19:39668600-39674400	Weak transcription	Aorta	Aorta
9	chr19:39669000-39674800	Weak transcription	HUVEC	blood vessel
10	chr19:39669200-39685800	Weak transcription	NHEK	skin
11	chr19:39669400-39675800	Weak transcription	Hela-S3	cervix
12	chr19:39669400-39676000	Weak transcription	Primary T cells fromperipheralblood	blood
13	chr19:39669400-39678200	Weak transcription	Primary T helper cells PMA-I stimulated	--
14	chr19:39669600-39674800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr19:39669600-39675400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr19:39669600-39677800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr19:39669600-39678200	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr19:39669800-39676000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr19:39669800-39678200	Weak transcription	Right Ventricle	heart
20	chr19:39670000-39675000	Weak transcription	Primary neutrophils fromperipheralblood	blood
21	chr19:39670600-39678400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr19:39670800-39678200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr19:39671000-39674200	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr19:39671000-39674200	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr19:39671000-39674200	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr19:39671000-39674800	Weak transcription	Primary T cells from cord blood	blood
27	chr19:39671000-39675200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr19:39671000-39675200	Weak transcription	Monocytes-CD14+_RO01746	blood
29	chr19:39671000-39675800	Weak transcription	Brain Hippocampus Middle	brain
30	chr19:39671000-39676000	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr19:39671000-39678200	Weak transcription	Esophagus	oesophagus
32	chr19:39671000-39678400	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr19:39671000-39678400	Weak transcription	Spleen	Spleen
34	chr19:39671200-39674200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr19:39671200-39675000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr19:39671600-39675000	Weak transcription	Osteobl	bone
37	chr19:39671600-39675400	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr19:39671600-39675800	Weak transcription	Thymus	Thymus
39	chr19:39672000-39674200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr19:39672000-39677800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr19:39672000-39677800	Weak transcription	Duodenum Mucosa	Duodenum
42	chr19:39672000-39683600	Weak transcription	Pancreas	Pancrea
43	chr19:39672200-39675000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr19:39672400-39675000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr19:39672400-39676200	Weak transcription	Colonic Mucosa	Colon
46	chr19:39672400-39677800	Weak transcription	Fetal Intestine Large	intestine
47	chr19:39672400-39678200	Weak transcription	Lung	lung
48	chr19:39672600-39676200	Weak transcription	NHLF	lung
49	chr19:39672600-39677200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
50	chr19:39672600-39678200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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