Variant report

Variant	rs3177673
Chromosome Location	chr9:19049512-19049513
allele	G/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:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:19047624..19049710-chr9:19124952..19127835,2	MCF-7	breast:
2	chr9:19048660..19050563-chr9:19101012..19103938,3	MCF-7	breast:
3	chr9:19047048..19050954-chr9:19228997..19232024,5	K562	blood:
4	chr9:19049459..19051000-chr9:19381745..19383775,2	K562	blood:
5	chr9:19048960..19051096-chr9:19378749..19380850,2	MCF-7	breast:
6	chr12:118810455..118810963-chr9:19049262..19049813,2	NB4	blood:
7	chr6:111136556..111137100-chr9:19049267..19049877,2	NB4	blood:
8	chr9:19049276..19051385-chr9:19371232..19373694,3	MCF-7	breast:
9	chr3:122134669..122135507-chr9:19049217..19049843,2	Hela-S3	cervix:
10	chr9:19049042..19049712-chrX:153284604..153285345,2	Hela-S3	cervix:
11	chr9:19047789..19050837-chr9:19378682..19381375,3	MCF-7	breast:
12	chr9:19048684..19049542-chr9:100684339..100685327,2	Hela-S3	cervix:
13	chr9:19047688..19050062-chr9:19125989..19129041,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000147872	Chromatin interaction
ENSG00000155111	Chromatin interaction
ENSG00000137145	Chromatin interaction
ENSG00000272758	Chromatin interaction
ENSG00000136932	Chromatin interaction
ENSG00000147874	Chromatin interaction
ENSG00000196981	Chromatin interaction
ENSG00000272842	Chromatin interaction
ENSG00000184216	Chromatin interaction
ENSG00000135090	Chromatin interaction
ENSG00000137154	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10117419	1.00[ASN][1000 genomes]
rs10117445	1.00[ASN][1000 genomes]
rs10811096	0.85[EUR][1000 genomes]
rs10963937	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11496354	0.83[AMR][1000 genomes]
rs17236157	0.85[EUR][1000 genomes]
rs2233800	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4478656	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62560398	0.85[EUR][1000 genomes]
rs62560399	0.85[EUR][1000 genomes]
rs62560432	0.85[EUR][1000 genomes]
rs7858899	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs883440	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1017820	chr9:18882219-19587377	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
2	nsv540078	chr9:18882219-19587377	Genic enhancers Transcr. at gene 5' and 3' Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
3	nsv892700	chr9:18979441-19156784	Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv973452	chr9:19033958-19053096	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
5	nsv1028623	chr9:19034742-19394712	Strong transcription Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
6	nsv540079	chr9:19034742-19394712	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3177673	ENSG00000155876	cis	multi-tissue	Pritchard

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:19048000-19050600	Active TSS	HUES64 Cell Line	embryonic stem cell
2	chr9:19048200-19050400	Active TSS	HSMM	muscle
3	chr9:19048400-19050000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr9:19048400-19050200	Active TSS	H1 Cell Line	embryonic stem cell
5	chr9:19048400-19050200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr9:19048400-19050400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr9:19048400-19050400	Active TSS	Colon Smooth Muscle	Colon
8	chr9:19048400-19050600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr9:19048400-19050600	Active TSS	Brain Anterior Caudate	brain
10	chr9:19048400-19050600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
11	chr9:19048400-19050800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr9:19048400-19050800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
13	chr9:19048400-19050800	Active TSS	A549	lung
14	chr9:19048400-19051000	Active TSS	Fetal Kidney	kidney
15	chr9:19048400-19051000	Active TSS	K562	blood
16	chr9:19048400-19051000	Active TSS	NHDF-Ad	bronchial
17	chr9:19048400-19051200	Active TSS	ES-I3 Cell Line	embryonic stem cell
18	chr9:19048400-19051200	Active TSS	H9 Cell Line	embryonic stem cell
19	chr9:19048400-19051200	Active TSS	Colonic Mucosa	Colon
20	chr9:19048400-19051200	Active TSS	Right Ventricle	heart
21	chr9:19048400-19051400	Active TSS	iPS-15b Cell Line	embryonic stem cell
22	chr9:19048400-19051600	Active TSS	iPS-18 Cell Line	embryonic stem cell
23	chr9:19048400-19051600	Active TSS	Pancreatic Islets	Pancreatic Islet
24	chr9:19048400-19051800	Active TSS	HUES48 Cell Line	embryonic stem cell
25	chr9:19048400-19051800	Active TSS	HUES6 Cell Line	embryonic stem cell
26	chr9:19048600-19050400	Active TSS	iPS-20b Cell Line	embryonic stem cell
27	chr9:19048600-19050400	Active TSS	Fetal Brain Male	brain
28	chr9:19048600-19050600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr9:19048600-19050600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr9:19048600-19050600	Active TSS	Fetal Brain Female	brain
31	chr9:19048600-19050600	Bivalent/Poised TSS	HepG2	liver
32	chr9:19048600-19050600	Active TSS	HSMMtube	muscle
33	chr9:19048600-19050800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr9:19048600-19050800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr9:19048600-19050800	Active TSS	Sigmoid Colon	Sigmoid Colon
36	chr9:19048600-19050800	Active TSS	Thymus	Thymus
37	chr9:19048600-19051000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
38	chr9:19048600-19051000	Active TSS	Breast Myoepithelial Primary Cells	Breast
39	chr9:19048600-19051000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr9:19048600-19051000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr9:19048600-19051200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr9:19048600-19051200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr9:19048600-19051200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr9:19048600-19051200	Active TSS	Psoas Muscle	Psoas
45	chr9:19048600-19051200	Active TSS	Right Atrium	heart
46	chr9:19048600-19051200	Active TSS	GM12878-XiMat	blood
47	chr9:19048600-19051400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr9:19048800-19049600	Active TSS	Skeletal Muscle Female	skeletal muscle
49	chr9:19048800-19050000	Active TSS	Brain Angular Gyrus	brain
50	chr9:19048800-19050200	Active TSS	Brain Hippocampus Middle	brain

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