Variant report

Variant	rs33940778
Chromosome Location	chr15:77360023-77360024
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:77359065..77361270-chr15:77362713..77364449,3	K562	blood:
2	chr15:77357220..77360797-chr15:77361367..77364060,6	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PEAK1.1-4	chr15:77359996-77360667	ENSG00000269951.1

Variant related genes	Relation type
ENSG00000140391	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11630837	0.85[JPT][hapmap]
rs11632999	0.85[JPT][hapmap]
rs11636648	0.85[YRI][hapmap]
rs11638220	0.85[JPT][hapmap]
rs11639079	0.85[JPT][hapmap]
rs11639197	0.85[JPT][hapmap]
rs12148612	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12904328	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12904384	0.85[JPT][hapmap]
rs12909704	0.85[JPT][hapmap]
rs12910419	0.85[JPT][hapmap]
rs17382798	0.85[JPT][hapmap]
rs17466989	0.85[JPT][hapmap]
rs33931897	0.96[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7169831	0.85[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3440794	chr15:76764595-77571114	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer 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	25 gene(s)	inside rSNPs	diseases
2	esv3367577	chr15:77015618-77442634	Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv1040852	chr15:77160237-78137541	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
4	esv2758388	chr15:77170550-77373448	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS 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	18 gene(s)	inside rSNPs	diseases
5	esv2760041	chr15:77170550-77373448	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv833058	chr15:77235895-77393640	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv517068	chr15:77254544-77381222	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
8	nsv904414	chr15:77304310-77400388	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
9	nsv1045376	chr15:77354671-77801487	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh 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
10	nsv542443	chr15:77354671-77801487	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription 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	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs33940778	HMG20A	cis	cerebellum	SCAN
rs33940778	SGK269	cis	parietal	SCAN
rs33940778	STRA6	cis	cerebellum	SCAN
rs33940778	HMG20A	cis	parietal	SCAN
rs33940778	RP11-797A18.4	cis	Artery Tibial	GTEx

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77321200-77362000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr15:77339000-77362000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr15:77345200-77360200	Weak transcription	Spleen	Spleen
4	chr15:77345200-77362000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr15:77345400-77361400	Weak transcription	Placenta	Placenta
6	chr15:77346600-77361200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr15:77347200-77361600	Weak transcription	Dnd41	blood
8	chr15:77349200-77362000	Weak transcription	Lung	lung
9	chr15:77349400-77361000	Weak transcription	Fetal Thymus	thymus
10	chr15:77349600-77362000	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr15:77351000-77361800	Weak transcription	Pancreas	Pancrea
12	chr15:77352400-77362000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr15:77352600-77360200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr15:77352600-77362000	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr15:77353000-77361800	Weak transcription	Thymus	Thymus
16	chr15:77353200-77361800	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr15:77353400-77361600	Weak transcription	Primary T cells from cord blood	blood
18	chr15:77353800-77360200	Enhancers	Stomach Mucosa	stomach
19	chr15:77353800-77362000	Weak transcription	Left Ventricle	heart
20	chr15:77354000-77361800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr15:77354000-77361800	Weak transcription	Fetal Muscle Trunk	muscle
22	chr15:77354200-77362000	Weak transcription	Aorta	Aorta
23	chr15:77354400-77361000	Weak transcription	Fetal Muscle Leg	muscle
24	chr15:77354400-77361800	Weak transcription	Right Atrium	heart
25	chr15:77354400-77362000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr15:77354600-77360200	Weak transcription	Fetal Brain Female	brain
27	chr15:77354800-77360200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr15:77355200-77361200	Weak transcription	Fetal Stomach	stomach
29	chr15:77355800-77362000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
30	chr15:77356200-77361000	Enhancers	Fetal Intestine Large	intestine
31	chr15:77357200-77361800	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr15:77357200-77361800	Weak transcription	Primary neutrophils fromperipheralblood	blood
33	chr15:77357200-77362000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr15:77357400-77361000	Weak transcription	Brain Substantia Nigra	brain
35	chr15:77357400-77361800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr15:77357400-77362000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr15:77357600-77360200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr15:77357600-77360200	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr15:77357600-77360600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr15:77357600-77361800	Weak transcription	HMEC	breast
41	chr15:77357600-77362000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
42	chr15:77358000-77360600	Enhancers	Colonic Mucosa	Colon
43	chr15:77358400-77361800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr15:77358400-77362000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr15:77358600-77360200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr15:77358600-77362200	Enhancers	Sigmoid Colon	Sigmoid Colon
47	chr15:77358800-77361600	Enhancers	HUVEC	blood vessel
48	chr15:77358800-77362000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr15:77359000-77360200	Enhancers	Monocytes-CD14+_RO01746	blood
50	chr15:77359000-77361000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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