Variant report

Variant	rs3730179
Chromosome Location	chr19:18277206-18277207
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:18277023-18277244	K562	blood:	n/a	n/a
2	POLR2A	chr19:18277101-18277400	HepG2	liver:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:18275011..18277551-chr19:18282905..18285760,2	MCF-7	breast:
2	chr19:18264048..18266866-chr19:18276838..18280987,4	K562	blood:
3	chr19:18269687..18274074-chr19:18275310..18278985,6	MCF-7	breast:
4	chr19:18276990..18278607-chr19:18389377..18392205,2	K562	blood:
5	chr19:18260584..18267400-chr19:18276077..18285960,14	MCF-7	breast:
6	chr19:18275085..18277218-chr19:18301566..18304039,2	K562	blood:

No data

Variant related genes	Relation type
PIK3R2	TF binding region
ENSG00000216490	Chromatin interaction
ENSG00000130522	Chromatin interaction
ENSG00000254858	Chromatin interaction
ENSG00000268173	Chromatin interaction
ENSG00000269145	Chromatin interaction
ENSG00000105647	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs12052085	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2173006	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs273496	0.85[CEU][hapmap];0.81[MEX][hapmap]
rs273512	0.85[CEU][hapmap];0.82[TSI][hapmap]
rs3746187	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55989116	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62123609	0.82[ASN][1000 genomes]
rs62123615	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62123617	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:28 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1055932	chr19:17923918-18369944	Weak transcription Strong transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
2	nsv543923	chr19:17923918-18369944	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats 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	109 gene(s)	inside rSNPs	diseases
3	nsv532614	chr19:18033043-18573963	Flanking Active TSS Enhancers Active TSS Genic enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	204 gene(s)	inside rSNPs	diseases
4	esv1837595	chr19:18085428-18393682	Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	147 gene(s)	inside rSNPs	diseases
5	nsv833773	chr19:18152971-18302988	Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
6	nsv911241	chr19:18193191-18304700	Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
7	nsv911242	chr19:18201757-18304700	Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
8	nsv911243	chr19:18206681-18283501	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
9	nsv911244	chr19:18206681-18304700	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
10	nsv911245	chr19:18206681-18338101	Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
11	nsv833774	chr19:18213761-18295329	Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
12	nsv833775	chr19:18213761-18390074	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
13	nsv911246	chr19:18224729-18283501	Weak transcription Genic enhancers Flanking Active TSS Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
14	nsv911247	chr19:18224729-18288069	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
15	nsv911248	chr19:18224729-18338101	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
16	nsv911249	chr19:18224729-18375846	Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
17	nsv911250	chr19:18224729-18376522	Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
18	nsv911251	chr19:18224729-18422364	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
19	nsv2429	chr19:18234179-18279381	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
20	nsv911252	chr19:18234588-18338101	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
21	nsv911253	chr19:18240127-18418044	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
22	nsv916325	chr19:18244780-18534927	Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	167 gene(s)	inside rSNPs	diseases
23	nsv911254	chr19:18248146-18310678	Enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
24	nsv911255	chr19:18254876-18282586	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
25	nsv911256	chr19:18255359-18338101	Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
26	nsv911257	chr19:18258598-18282586	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription 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	23 gene(s)	inside rSNPs	diseases
27	nsv911258	chr19:18262371-18282586	Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
28	nsv911259	chr19:18264940-18283501	Strong transcription Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs3730179	SNORA68	cis	cerebellum	SCAN
rs3730179	HAPLN4	cis	cerebellum	SCAN
rs3730179	ANKLE1	cis	cerebellum	SCAN
rs3730179	TM6SF2	cis	cerebellum	SCAN
rs3730179	ZNF714	cis	parietal	SCAN
rs3730179	HSH2D	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:18265000-18284200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr19:18270800-18282000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr19:18271800-18279800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr19:18272600-18281800	Strong transcription	Cortex derived primary cultured neurospheres	brain
5	chr19:18272600-18282600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr19:18272800-18278000	Weak transcription	NHDF-Ad	bronchial
7	chr19:18272800-18278800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr19:18272800-18278800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr19:18272800-18278800	Strong transcription	Spleen	Spleen
10	chr19:18272800-18279200	Strong transcription	Fetal Stomach	stomach
11	chr19:18272800-18279800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
12	chr19:18272800-18280000	Strong transcription	Brain Anterior Caudate	brain
13	chr19:18272800-18280200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr19:18272800-18280400	Strong transcription	Rectal Mucosa Donor 29	rectum
15	chr19:18272800-18280600	Strong transcription	HUES6 Cell Line	embryonic stem cell
16	chr19:18272800-18280600	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chr19:18272800-18280600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr19:18272800-18280600	Strong transcription	Liver	Liver
19	chr19:18272800-18280600	Strong transcription	Dnd41	blood
20	chr19:18272800-18281000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr19:18272800-18281000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr19:18272800-18281200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr19:18272800-18281800	Strong transcription	H1 Cell Line	embryonic stem cell
24	chr19:18272800-18281800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr19:18272800-18282000	Strong transcription	Brain Germinal Matrix	brain
26	chr19:18272800-18282000	Strong transcription	Thymus	Thymus
27	chr19:18272800-18282200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
28	chr19:18272800-18282600	Strong transcription	Fetal Brain Female	brain
29	chr19:18272800-18282800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr19:18272800-18282800	Strong transcription	H9 Cell Line	embryonic stem cell
31	chr19:18272800-18282800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr19:18272800-18284200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr19:18272800-18284200	Weak transcription	Right Atrium	heart
34	chr19:18272800-18284200	Weak transcription	Stomach Mucosa	stomach
35	chr19:18272800-18284600	Weak transcription	Small Intestine	intestine
36	chr19:18273000-18278200	Strong transcription	Rectal Smooth Muscle	rectum
37	chr19:18273000-18278800	Strong transcription	Primary T cells fromperipheralblood	blood
38	chr19:18273000-18279200	Strong transcription	Placenta	Placenta
39	chr19:18273000-18279800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr19:18273000-18280200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr19:18273000-18280400	Strong transcription	Brain Cingulate Gyrus	brain
42	chr19:18273000-18280600	Strong transcription	Brain Inferior Temporal Lobe	brain
43	chr19:18273000-18280600	Strong transcription	Duodenum Mucosa	Duodenum
44	chr19:18273000-18280800	Strong transcription	Brain Hippocampus Middle	brain
45	chr19:18273000-18280800	Strong transcription	Fetal Thymus	thymus
46	chr19:18273000-18280800	Strong transcription	Osteobl	bone
47	chr19:18273000-18281800	Strong transcription	Fetal Intestine Small	intestine
48	chr19:18273000-18282400	Weak transcription	Fetal Heart	heart
49	chr19:18273000-18282600	Strong transcription	Fetal Intestine Large	intestine
50	chr19:18273000-18282800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell

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