Variant report

Variant	rs7298613
Chromosome Location	chr12:104690163-104690164
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:104571599..104574180-chr12:104689003..104690549,2	MCF-7	breast:
2	chr12:104528933..104532757-chr12:104688299..104690796,3	MCF-7	breast:
3	chr12:104688661..104692008-chr12:104701962..104705113,4	MCF-7	breast:
4	chr12:104689111..104691925-chr12:104705420..104707657,2	MCF-7	breast:
5	chr12:104614582..104616135-chr12:104689398..104692216,2	MCF-7	breast:
6	chr12:104679689..104685346-chr12:104688497..104691899,10	MCF-7	breast:
7	chr12:104599765..104602072-chr12:104689282..104691994,2	MCF-7	breast:
8	chr12:104688038..104691573-chr12:104694221..104698678,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000120837	Chromatin interaction
ENSG00000198431	Chromatin interaction
ENSG00000255150	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10735392	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10735393	0.91[EUR][1000 genomes]
rs10735395	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10745995	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10745996	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10861204	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11111943	0.91[AMR][1000 genomes]
rs11111983	0.83[AMR][1000 genomes]
rs12426783	0.90[EUR][1000 genomes]
rs3935021	0.82[EUR][1000 genomes]
rs4129598	0.81[AMR][1000 genomes]
rs4246264	0.91[AMR][1000 genomes]
rs4246269	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4246270	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4246271	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4388968	0.91[AMR][1000 genomes]
rs4447242	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4502051	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4545635	0.91[AMR][1000 genomes]
rs4614534	0.80[AMR][1000 genomes]
rs4630362	0.90[EUR][1000 genomes]
rs4964257	0.91[AMR][1000 genomes]
rs4964260	0.91[AMR][1000 genomes]
rs4964288	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4964741	0.98[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4964752	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4964761	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4964779	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4964784	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6419386	0.91[AMR][1000 genomes]
rs6539128	0.81[AMR][1000 genomes]
rs6539137	0.90[EUR][1000 genomes]
rs7132418	0.82[AMR][1000 genomes]
rs7138035	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7138317	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7139336	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7294997	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7295413	0.83[AMR][1000 genomes]
rs7303483	0.86[AMR][1000 genomes]
rs7305872	0.84[AMR][1000 genomes]
rs73181916	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73181919	0.91[EUR][1000 genomes]
rs73181926	0.91[EUR][1000 genomes]
rs7962423	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7969351	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7969604	0.90[EUR][1000 genomes]
rs7972034	0.80[AMR][1000 genomes]
rs7978101	0.84[AMR][1000 genomes]
rs9738614	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9739826	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9739833	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899493	chr12:104548613-104703228	Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv899494	chr12:104561521-104806232	Flanking Active TSS Weak transcription Genic enhancers Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv1046606	chr12:104606617-104763734	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv1038609	chr12:104613847-104764981	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv541587	chr12:104613847-104764981	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7298613	NFYB	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104683400-104696800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr12:104683600-104690200	Weak transcription	Fetal Kidney	kidney
3	chr12:104683800-104690400	Strong transcription	Fetal Muscle Trunk	muscle
4	chr12:104683800-104693800	Weak transcription	Fetal Heart	heart
5	chr12:104683800-104696600	Weak transcription	Brain Anterior Caudate	brain
6	chr12:104683800-104696800	Weak transcription	Fetal Brain Male	brain
7	chr12:104683800-104697000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr12:104683800-104723800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr12:104684200-104693400	Strong transcription	Fetal Thymus	thymus
10	chr12:104684200-104696600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr12:104684400-104696600	Weak transcription	Right Atrium	heart
12	chr12:104684600-104694400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr12:104684600-104694800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
14	chr12:104684800-104690400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr12:104684800-104690800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr12:104684800-104693000	Strong transcription	Primary monocytes fromperipheralblood	blood
17	chr12:104684800-104693200	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr12:104685000-104695000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr12:104685400-104690800	Strong transcription	Fetal Muscle Leg	muscle
20	chr12:104685400-104691800	Strong transcription	Primary T cells from cord blood	blood
21	chr12:104685600-104690200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr12:104685600-104690800	Strong transcription	Fetal Brain Female	brain
23	chr12:104685600-104691000	Strong transcription	Primary B cells from cord blood	blood
24	chr12:104685600-104691800	Strong transcription	Cortex derived primary cultured neurospheres	brain
25	chr12:104685800-104691800	Strong transcription	Thymus	Thymus
26	chr12:104685800-104696800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr12:104686000-104694200	Strong transcription	HUES48 Cell Line	embryonic stem cell
28	chr12:104686000-104696800	Weak transcription	Brain Angular Gyrus	brain
29	chr12:104686200-104696800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr12:104686200-104700600	Strong transcription	Dnd41	blood
31	chr12:104686400-104697600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr12:104686600-104692000	Strong transcription	Primary hematopoietic stem cells	blood
33	chr12:104686800-104694200	Strong transcription	HUES6 Cell Line	embryonic stem cell
34	chr12:104686800-104694400	Strong transcription	HUES64 Cell Line	embryonic stem cell
35	chr12:104686800-104696600	Weak transcription	Fetal Intestine Small	intestine
36	chr12:104687000-104691400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
37	chr12:104687200-104690800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr12:104687200-104696800	Weak transcription	Psoas Muscle	Psoas
39	chr12:104687200-104700600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr12:104687400-104696600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
41	chr12:104687400-104696600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr12:104687400-104696600	Weak transcription	Stomach Smooth Muscle	stomach
43	chr12:104687400-104697000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr12:104687600-104697400	Weak transcription	Gastric	stomach
45	chr12:104687800-104690600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr12:104688000-104694400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
47	chr12:104688000-104694400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
48	chr12:104688200-104690200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr12:104688200-104690800	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr12:104688200-104693000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell

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