Variant report

Variant	rs3941970
Chromosome Location	chr7:101427630-101427631
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:101409801..101412739-chr7:101427565..101429421,3	MCF-7	breast:
2	chr7:101426789..101430300-chr7:101456743..101460658,3	MCF-7	breast:
3	chr7:101427247..101429572-chr7:101431090..101433945,2	K562	blood:

Variant related genes	Relation type
ENSG00000257923	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs11763398	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11767979	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4585681	0.82[CEU][hapmap]
rs62463709	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62463710	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62463711	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933653	chr7:100701931-101515782	Active TSS ZNF genes & repeats Bivalent Enhancer Enhancers Genic enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
2	nsv831079	chr7:101273495-101466776	Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	nsv1021797	chr7:101342353-101466957	Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
4	nsv539046	chr7:101342353-101466957	Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
5	nsv1024319	chr7:101368299-101668159	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
6	nsv539047	chr7:101368299-101668159	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
7	nsv1020372	chr7:101420819-101718950	Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3941970	RINT1	cis	cerebellum	SCAN
rs3941970	PVRIG	cis	cerebellum	SCAN
rs3941970	PDAP1	cis	cerebellum	SCAN
rs3941970	MUC17	cis	parietal	SCAN

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:101420000-101436600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr7:101425600-101427800	Enhancers	Hela-S3	cervix
3	chr7:101425600-101428200	Enhancers	Placenta	Placenta
4	chr7:101425800-101427800	Enhancers	Stomach Mucosa	stomach
5	chr7:101426000-101429000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
6	chr7:101426400-101428200	Enhancers	Fetal Brain Male	brain
7	chr7:101426400-101428400	Enhancers	Brain Anterior Caudate	brain
8	chr7:101426400-101428600	Enhancers	Fetal Brain Female	brain
9	chr7:101426600-101427800	Enhancers	Duodenum Mucosa	Duodenum
10	chr7:101426800-101428000	Bivalent Enhancer	Adipose Nuclei	Adipose
11	chr7:101427000-101428200	Enhancers	Right Ventricle	heart
12	chr7:101427000-101428600	Enhancers	Fetal Heart	heart
13	chr7:101427200-101427800	Enhancers	Skeletal Muscle Male	skeletal muscle
14	chr7:101427200-101427800	Enhancers	Spleen	Spleen
15	chr7:101427200-101428000	Enhancers	Psoas Muscle	Psoas
16	chr7:101427200-101428200	Enhancers	Brain Angular Gyrus	brain
17	chr7:101427200-101428200	Enhancers	Fetal Muscle Trunk	muscle
18	chr7:101427200-101428200	Enhancers	Left Ventricle	heart
19	chr7:101427200-101428400	Enhancers	Ovary	ovary
20	chr7:101427200-101428400	Enhancers	Right Atrium	heart
21	chr7:101427400-101427800	Enhancers	Liver	Liver
22	chr7:101427400-101427800	Enhancers	Fetal Lung	lung
23	chr7:101427400-101427800	Bivalent Enhancer	K562	blood
24	chr7:101427400-101428200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr7:101427400-101428200	Enhancers	Lung	lung
26	chr7:101427400-101428200	Flanking Bivalent TSS/Enh	HepG2	liver
27	chr7:101427400-101428400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr7:101427400-101428400	Enhancers	Primary monocytes fromperipheralblood	blood
29	chr7:101427400-101428400	Enhancers	Primary hematopoietic stem cells	blood
30	chr7:101427400-101428400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr7:101427400-101428400	Enhancers	Brain Cingulate Gyrus	brain
32	chr7:101427400-101428400	Enhancers	Brain Hippocampus Middle	brain
33	chr7:101427400-101428400	Enhancers	Monocytes-CD14+_RO01746	blood
34	chr7:101427400-101428600	Enhancers	Primary hematopoietic stem cells short term culture	blood
35	chr7:101427600-101428000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr7:101427600-101428000	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr7:101427600-101428000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
38	chr7:101427600-101428200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr7:101427600-101428200	Enhancers	HSMMtube	muscle
40	chr7:101427600-101428400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr7:101427600-101428400	Enhancers	Fetal Kidney	kidney
42	chr7:101427600-101428400	Bivalent Enhancer	Fetal Muscle Leg	muscle
43	chr7:101427600-101428400	Enhancers	Fetal Thymus	thymus
44	chr7:101427600-101428600	Enhancers	HSMM	muscle

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