Variant report

Variant	rs7277840
Chromosome Location	chr21:40365504-40365505
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:40175721..40178451-chr21:40363610..40366022,2	MCF-7	breast:
2	chr21:40178699..40181140-chr21:40363859..40366639,2	MCF-7	breast:
3	chr21:40363729..40365519-chr21:40450933..40453714,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000157557	Chromatin interaction

Extended variants
information (count: 5 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs2836814	0.86[CEU][hapmap]
rs2836815	0.96[CEU][hapmap];0.92[MEX][hapmap];0.80[AMR][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	nsv1062425	chr21:40172471-40380976	Enhancers Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv544442	chr21:40172471-40380976	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv587477	chr21:40228920-40512004	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7277840	PIGP	cis	cerebellum	SCAN
rs7277840	RIPK4	cis	parietal	SCAN

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40352400-40370000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr21:40356000-40369400	Enhancers	Left Ventricle	heart
3	chr21:40357400-40376400	Enhancers	Primary hematopoietic stem cells short term culture	blood
4	chr21:40359800-40368400	Enhancers	Fetal Heart	heart
5	chr21:40360000-40369200	Enhancers	Fetal Lung	lung
6	chr21:40360000-40370000	Enhancers	Primary hematopoietic stem cells	blood
7	chr21:40360400-40368600	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr21:40360800-40369600	Enhancers	Fetal Thymus	thymus
9	chr21:40360800-40376600	Weak transcription	Gastric	stomach
10	chr21:40362000-40366400	Enhancers	Adipose Nuclei	Adipose
11	chr21:40362000-40368600	Enhancers	Fetal Stomach	stomach
12	chr21:40362000-40369600	Enhancers	Fetal Muscle Leg	muscle
13	chr21:40362200-40365800	Weak transcription	Liver	Liver
14	chr21:40362200-40366200	Enhancers	Colon Smooth Muscle	Colon
15	chr21:40362200-40367200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr21:40362200-40369200	Enhancers	Skeletal Muscle Male	skeletal muscle
17	chr21:40362400-40366600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr21:40362600-40368000	Enhancers	HepG2	liver
19	chr21:40362600-40376800	Weak transcription	Aorta	Aorta
20	chr21:40362800-40365600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr21:40362800-40365800	Weak transcription	Psoas Muscle	Psoas
22	chr21:40362800-40367000	Enhancers	Stomach Smooth Muscle	stomach
23	chr21:40362800-40367200	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr21:40362800-40367600	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr21:40362800-40367600	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr21:40363600-40365600	Weak transcription	Rectal Smooth Muscle	rectum
27	chr21:40363600-40367000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr21:40363600-40367000	Enhancers	Right Atrium	heart
29	chr21:40363600-40367200	Enhancers	Skeletal Muscle Female	skeletal muscle
30	chr21:40363600-40375800	Weak transcription	Colonic Mucosa	Colon
31	chr21:40363800-40366800	Enhancers	HMEC	breast
32	chr21:40363800-40367600	Weak transcription	Dnd41	blood
33	chr21:40364000-40367000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr21:40364200-40365800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr21:40364200-40365800	Enhancers	Primary monocytes fromperipheralblood	blood
36	chr21:40364200-40366800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr21:40364200-40366800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr21:40364200-40366800	Enhancers	Fetal Kidney	kidney
39	chr21:40364200-40367800	Weak transcription	Thymus	Thymus
40	chr21:40364400-40365800	Enhancers	Brain Hippocampus Middle	brain
41	chr21:40364400-40366200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr21:40364400-40366200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr21:40364400-40366200	Enhancers	NH-A	brain
44	chr21:40364400-40366400	Enhancers	Small Intestine	intestine
45	chr21:40364400-40366600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr21:40364400-40366800	Enhancers	NHDF-Ad	bronchial
47	chr21:40364400-40367600	Enhancers	Placenta Amnion	Placenta Amnion
48	chr21:40364600-40365600	Weak transcription	Pancreas	Pancrea
49	chr21:40364600-40365600	Weak transcription	Right Ventricle	heart
50	chr21:40364600-40366000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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