Variant report

Variant	rs16847813
Chromosome Location	chr1:227618915-227618916
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZNF384	chr1:227618633-227618960	K562	blood:	n/a	n/a
2	STAT3	chr1:227618844-227618956	MCF10A-Er-Src	breast:	n/a	n/a
3	GATA3	chr1:227618618-227619013	T-47D	breast:	n/a	chr1:227618893-227618900 chr1:227618893-227618900 chr1:227618741-227618749 chr1:227618893-227618900
4	CEBPB	chr1:227618883-227619082	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:227504042..227507688-chr1:227616722..227620233,4	K562	blood:
2	chr1:227616535..227618369-chr1:227618757..227620375,2	MCF-7	breast:
3	chr1:227505302..227507077-chr1:227617949..227620450,2	MCF-7	breast:
4	chr1:227615748..227618335-chr1:227618739..227621470,2	MCF-7	breast:
5	chr1:227506036..227507932-chr1:227615818..227619997,3	MCF-7	breast:

Variant related genes	Relation type
BTF3P9	TF binding region
ENSG00000242757	Chromatin interaction
ENSG00000143776	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs12028062	0.85[CHB][hapmap]
rs16847790	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4418564	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6426452	0.84[EUR][1000 genomes];0.88[ASN][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	nsv534002	chr1:227315186-228047108	Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
2	nsv1001353	chr1:227474785-227660691	Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv1003278	chr1:227563126-227678464	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs16847813	NVL	cis	parietal	SCAN
rs16847813	CAPN2	cis	parietal	SCAN
rs16847813	OBSCN	cis	cerebellum	SCAN

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227615200-227619400	Enhancers	Brain Hippocampus Middle	brain
2	chr1:227615200-227619600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr1:227615200-227621000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
4	chr1:227615400-227619400	Enhancers	Brain Anterior Caudate	brain
5	chr1:227615400-227623400	Enhancers	Brain Cingulate Gyrus	brain
6	chr1:227615600-227621000	Enhancers	Brain Inferior Temporal Lobe	brain
7	chr1:227616000-227619200	Enhancers	Brain Substantia Nigra	brain
8	chr1:227616000-227622200	Enhancers	Fetal Muscle Leg	muscle
9	chr1:227616200-227619400	Enhancers	Skeletal Muscle Male	skeletal muscle
10	chr1:227616200-227619800	Enhancers	ES-I3 Cell Line	embryonic stem cell
11	chr1:227616200-227620000	Enhancers	Fetal Muscle Trunk	muscle
12	chr1:227616400-227620000	Enhancers	HUES6 Cell Line	embryonic stem cell
13	chr1:227616400-227621000	Enhancers	Lung	lung
14	chr1:227616600-227619400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr1:227616600-227619400	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr1:227616600-227625200	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr1:227616800-227619400	Enhancers	Skeletal Muscle Female	skeletal muscle
18	chr1:227616800-227619400	Weak transcription	Hela-S3	cervix
19	chr1:227617200-227619400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr1:227617400-227619200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr1:227617400-227619200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr1:227617400-227619600	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr1:227617400-227620800	Weak transcription	Spleen	Spleen
24	chr1:227617400-227625200	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr1:227617600-227619000	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr1:227617600-227619200	Weak transcription	Right Ventricle	heart
27	chr1:227617600-227619400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr1:227617600-227619400	Weak transcription	Gastric	stomach
29	chr1:227617600-227619400	Weak transcription	Stomach Smooth Muscle	stomach
30	chr1:227617600-227619600	Weak transcription	Pancreas	Pancrea
31	chr1:227617600-227621400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr1:227617600-227624000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr1:227617600-227624400	Weak transcription	Fetal Lung	lung
34	chr1:227617600-227625200	Weak transcription	Primary hematopoietic stem cells	blood
35	chr1:227617600-227625200	Weak transcription	Fetal Intestine Small	intestine
36	chr1:227617600-227631200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr1:227617800-227619200	Weak transcription	Colon Smooth Muscle	Colon
38	chr1:227617800-227619200	Weak transcription	Fetal Brain Male	brain
39	chr1:227617800-227619400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr1:227617800-227619400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr1:227617800-227619400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr1:227617800-227625200	Weak transcription	Fetal Kidney	kidney
43	chr1:227617800-227625200	Weak transcription	Psoas Muscle	Psoas
44	chr1:227617800-227625200	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr1:227617800-227625200	Weak transcription	Rectal Smooth Muscle	rectum
46	chr1:227618000-227619200	Weak transcription	Fetal Stomach	stomach
47	chr1:227618000-227619400	Enhancers	A549	lung
48	chr1:227618000-227624600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr1:227618000-227625200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr1:227618200-227619200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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