Variant report

Variant	rs2677778
Chromosome Location	chr4:16003175-16003176
allele	C/T
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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:15883971..15884920-chr4:16002717..16003637,2	K562	blood:
2	chr4:15957710..15958581-chr4:16002715..16003606,2	MCF-7	breast:
3	chr4:15964661..15965388-chr4:16002957..16003691,4	MCF-7	breast:
4	chr4:15964453..15965435-chr4:16002730..16004002,7	MCF-7	breast:
5	chr4:15965661..15966370-chr4:16002923..16003649,3	MCF-7	breast:
6	chr4:15884412..15887141-chr4:16001687..16004364,2	MCF-7	breast:
7	chr4:15994705..15996377-chr4:16001916..16003679,2	MCF-7	breast:
8	chr4:15807510..15808449-chr4:16002625..16003288,4	MCF-7	breast:
9	chr4:15965928..15966496-chr4:16002791..16003624,3	MCF-7	breast:
10	chr4:15479978..15480805-chr4:16002697..16003703,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000137441	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10003313	0.83[EUR][1000 genomes]
rs11726546	1.00[CEU][hapmap]
rs2058146	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2058147	1.00[CEU][hapmap];0.87[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2240683	1.00[CEU][hapmap];0.83[TSI][hapmap];0.94[EUR][1000 genomes]
rs2240684	1.00[CEU][hapmap];0.87[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2302167	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs28421727	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4698132	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4698437	0.83[AMR][1000 genomes]
rs6449212	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7659341	1.00[YRI][hapmap]
rs9991714	1.00[CEU][hapmap];0.83[EUR][1000 genomes]

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	nsv1012988	chr4:15597510-16091527	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv916742	chr4:15797994-16064232	Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2677778	PRSS30P	trans	lymphoblastoid	seeQTL

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:15964600-16031000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr4:15969600-16011600	Weak transcription	Fetal Lung	lung
3	chr4:15971000-16008000	Weak transcription	Aorta	Aorta
4	chr4:15977000-16007400	Weak transcription	Gastric	stomach
5	chr4:15978200-16003200	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr4:15982200-16008200	Weak transcription	Brain Germinal Matrix	brain
7	chr4:15988400-16033800	Weak transcription	Pancreas	Pancrea
8	chr4:15989000-16008000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr4:15989000-16014400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr4:15989000-16024200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr4:15990000-16015200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr4:15991000-16029000	Weak transcription	Stomach Mucosa	stomach
13	chr4:15992400-16003200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr4:15992800-16024800	Weak transcription	Fetal Intestine Small	intestine
15	chr4:15994800-16007200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr4:15995000-16003200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
17	chr4:15995000-16003200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr4:15995000-16003200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr4:15995400-16007200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr4:15995400-16007800	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr4:15996800-16007400	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr4:15996800-16008000	Weak transcription	Colonic Mucosa	Colon
23	chr4:15997000-16006800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr4:15999800-16004000	Weak transcription	Fetal Muscle Trunk	muscle
25	chr4:16000000-16003200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr4:16000000-16007000	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr4:16000200-16005400	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr4:16001800-16007200	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr4:16002000-16004000	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr4:16002000-16006400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr4:16002200-16004600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr4:16002400-16003600	Weak transcription	Primary hematopoietic stem cells	blood
33	chr4:16002400-16003600	Enhancers	Duodenum Smooth Muscle	Duodenum
34	chr4:16002400-16003600	Genic enhancers	Fetal Stomach	stomach
35	chr4:16002600-16003400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr4:16002600-16003400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
37	chr4:16002600-16003400	Enhancers	Brain Hippocampus Middle	brain
38	chr4:16002600-16003400	Enhancers	Fetal Brain Female	brain
39	chr4:16002600-16003400	Enhancers	Left Ventricle	heart
40	chr4:16002600-16003400	Enhancers	Right Atrium	heart
41	chr4:16002600-16003600	Enhancers	Brain Anterior Caudate	brain
42	chr4:16002600-16009400	Weak transcription	Fetal Brain Male	brain
43	chr4:16002800-16003200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr4:16002800-16003200	Enhancers	Thymus	Thymus
45	chr4:16002800-16003400	Enhancers	ES-I3 Cell Line	embryonic stem cell
46	chr4:16002800-16003400	Enhancers	HUES6 Cell Line	embryonic stem cell
47	chr4:16002800-16003400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
48	chr4:16002800-16003400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
49	chr4:16002800-16003400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
50	chr4:16002800-16003400	Enhancers	Right Ventricle	heart

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