Variant report

Variant	rs4939672
Chromosome Location	chr18:45452557-45452558
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr18:45452368-45453771	GM12878	blood:	n/a	n/a
2	GATA1	chr18:45452159-45453214	PBDE	blood:	n/a	n/a
3	JUND	chr18:45452418-45453079	K562	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr18:45425101..45428042-chr18:45452196..45454277,2	MCF-7	breast:
2	chr18:45444480..45447818-chr18:45450638..45453118,3	K562	blood:
3	chr18:45451758..45454511-chr18:45455218..45457678,2	MCF-7	breast:
4	chr18:45441870..45444292-chr18:45451454..45453055,2	MCF-7	breast:
5	chr18:45450692..45455196-chr18:45455930..45459309,6	MCF-7	breast:
6	chr18:45452201..45455106-chr18:45476820..45479374,2	MCF-7	breast:

No data

Variant related genes	Relation type
SMAD2	TF binding region
ENSG00000175387	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10432199	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10502890	0.82[EUR][1000 genomes]
rs10853560	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11082638	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11082639	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11874858	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12457664	0.83[EUR][1000 genomes]
rs12604337	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12605333	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12956483	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12968107	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1539872	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1573362	0.83[EUR][1000 genomes]
rs1573363	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1613672	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1631576	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17741998	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1787176	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1787193	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1787194	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1787196	0.84[EUR][1000 genomes]
rs1787197	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1792653	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1792655	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1792669	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1792670	0.89[EUR][1000 genomes]
rs1792672	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1792675	0.85[EUR][1000 genomes]
rs1792683	0.87[EUR][1000 genomes]
rs2000708	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2000709	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2012555	0.84[EUR][1000 genomes]
rs2096932	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2096933	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28548478	0.84[EUR][1000 genomes]
rs3813068	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4940109	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4940110	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4940120	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4940127	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61513611	0.80[EUR][1000 genomes]
rs62086544	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6507790	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7228393	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7231538	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7232764	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7232893	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7233129	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7236177	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7237544	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7243502	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs729112	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs747952	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs747953	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs765213	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8084915	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8095519	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8097580	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8097912	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8097925	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs8099127	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8099681	0.85[EUR][1000 genomes]
rs948600	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs948601	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs948603	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs948604	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9946556	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9947494	0.89[EUR][1000 genomes]
rs9950207	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9955626	0.83[EUR][1000 genomes]
rs9961652	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9966637	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9966964	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv909614	chr18:45419421-45478490	Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv909615	chr18:45452321-45493026	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:45433200-45455000	Weak transcription	Fetal Stomach	stomach
2	chr18:45433200-45455400	Weak transcription	Fetal Brain Male	brain
3	chr18:45434000-45454600	Weak transcription	Primary B cells from peripheral blood	blood
4	chr18:45435600-45455800	Weak transcription	Fetal Muscle Trunk	muscle
5	chr18:45438600-45454600	Enhancers	Primary T helper cells PMA-I stimulated	--
6	chr18:45438800-45453400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr18:45439000-45452800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr18:45439000-45452800	Weak transcription	Aorta	Aorta
9	chr18:45439000-45456200	Weak transcription	Esophagus	oesophagus
10	chr18:45439000-45456200	Weak transcription	Spleen	Spleen
11	chr18:45439200-45453000	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr18:45439200-45453400	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr18:45439600-45455400	Weak transcription	Fetal Muscle Leg	muscle
14	chr18:45439800-45452800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr18:45439800-45454600	Weak transcription	Fetal Intestine Large	intestine
16	chr18:45439800-45456200	Weak transcription	Pancreas	Pancrea
17	chr18:45441200-45453000	Weak transcription	Duodenum Mucosa	Duodenum
18	chr18:45442000-45454800	Weak transcription	Rectal Smooth Muscle	rectum
19	chr18:45442400-45452800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr18:45442400-45453400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr18:45442400-45453600	Weak transcription	NH-A	brain
22	chr18:45442400-45455000	Weak transcription	HSMM	muscle
23	chr18:45442600-45454600	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr18:45442800-45454400	Weak transcription	NHDF-Ad	bronchial
25	chr18:45443000-45456000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr18:45443600-45455000	Weak transcription	Osteobl	bone
27	chr18:45444400-45454400	Enhancers	Primary T cells from cord blood	blood
28	chr18:45444800-45453200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr18:45444800-45456000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr18:45444800-45456000	Weak transcription	Lung	lung
31	chr18:45445400-45453000	Weak transcription	NHEK	skin
32	chr18:45446000-45455400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
33	chr18:45446200-45454400	Weak transcription	Fetal Kidney	kidney
34	chr18:45446200-45455800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr18:45446600-45453600	Weak transcription	Monocytes-CD14+_RO01746	blood
36	chr18:45447600-45456000	Weak transcription	Left Ventricle	heart
37	chr18:45448000-45453000	Weak transcription	Brain Angular Gyrus	brain
38	chr18:45448400-45454400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr18:45448600-45453000	Weak transcription	Primary hematopoietic stem cells	blood
40	chr18:45448600-45453600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr18:45449400-45454800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
42	chr18:45450000-45452800	Weak transcription	Stomach Mucosa	stomach
43	chr18:45450000-45454400	Weak transcription	Primary B cells from cord blood	blood
44	chr18:45450000-45456200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr18:45450200-45452800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr18:45450200-45453200	Weak transcription	HMEC	breast
47	chr18:45450200-45453400	Weak transcription	Stomach Smooth Muscle	stomach
48	chr18:45450200-45453600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr18:45450200-45454600	Weak transcription	Ovary	ovary
50	chr18:45450200-45454800	Weak transcription	Right Atrium	heart

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