Variant report

Variant	rs6532774
Chromosome Location	chr4:99847952-99847953
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	JUN	chr4:99847877-99848064	H1-hESC	embryonic stem cell:	n/a	chr4:99847891-99847900
2	POLR2A	chr4:99847921-99848110	HepG2	liver:	n/a	n/a

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:99821499..99832064-chr4:99845860..99851281,12	MCF-7	breast:
2	chr4:99846410..99852563-chr4:99914756..99918771,11	MCF-7	breast:
3	chr4:99834371..99837889-chr4:99846144..99848239,3	MCF-7	breast:
4	chr4:99181196..99182841-chr4:99847002..99849754,2	MCF-7	breast:
5	chr4:99828711..99830237-chr4:99846843..99849645,2	MCF-7	breast:
6	chr4:99811621..99813284-chr4:99847831..99850392,2	MCF-7	breast:
7	chr4:99805865..99807821-chr4:99847875..99849598,2	MCF-7	breast:
8	chr4:99847842..99851448-chr4:99963294..99966988,3	K562	blood:
9	chr4:99834276..99835783-chr4:99846039..99848218,2	MCF-7	breast:
10	chr4:99842136..99852937-chr4:99913200..99922220,39	K562	blood:
11	chr4:99844460..99852883-chr4:99909835..99921707,41	K562	blood:

No data

Variant related genes	Relation type
ENSG00000263923	TF binding region
ENSG00000214559	Chromatin interaction
ENSG00000249055	Chromatin interaction
ENSG00000138698	Chromatin interaction
ENSG00000151247	Chromatin interaction
ENSG00000164024	Chromatin interaction
ENSG00000265213	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10007957	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10008093	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10010610	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10011791	0.93[ASN][1000 genomes]
rs10019506	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10020687	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10022521	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10032966	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10212891	0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1036946	1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs10433891	1.00[CHB][hapmap];0.88[JPT][hapmap];0.98[ASN][1000 genomes]
rs10433976	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10461135	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10470955	0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs10516437	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11725932	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11728783	0.95[ASN][1000 genomes]
rs11737130	0.94[ASN][1000 genomes]
rs11737186	0.94[ASN][1000 genomes]
rs1230147	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1230149	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1230150	0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1230152	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.89[JPT][hapmap];0.92[ASN][1000 genomes]
rs1230189	0.89[CHB][hapmap];0.85[CHD][hapmap];0.84[ASN][1000 genomes]
rs13110531	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17028238	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17028241	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17028244	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17028293	0.97[ASN][1000 genomes]
rs17550514	1.00[ASN][1000 genomes]
rs2602889	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28367437	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28376834	0.88[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs28430857	0.97[ASN][1000 genomes]
rs28473608	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28499420	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28529446	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28575093	0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs28577966	0.97[ASN][1000 genomes]
rs28589528	0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs28613604	0.97[ASN][1000 genomes]
rs28622595	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28633499	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3133161	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35447189	0.91[ASN][1000 genomes]
rs4699368	0.88[CEU][hapmap];0.81[AMR][1000 genomes]
rs4699370	0.83[ASN][1000 genomes]
rs60120090	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60658326	1.00[ASN][1000 genomes]
rs6815444	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6830125	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6841295	0.97[ASN][1000 genomes]
rs6846266	0.97[ASN][1000 genomes]
rs6846475	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs72677504	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72692622	0.98[ASN][1000 genomes]
rs7660937	0.99[ASN][1000 genomes]
rs7661487	0.97[ASN][1000 genomes]
rs7664964	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7666015	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7671306	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7671453	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7674319	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7676504	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7679685	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7684964	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7696573	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7696584	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7697071	0.97[ASN][1000 genomes]
rs9332467	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs994636	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9995478	0.92[ASN][1000 genomes]
rs9996959	0.96[ASN][1000 genomes]
rs9998221	0.85[AMR][1000 genomes]
rs9999702	0.93[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	nsv1009017	chr4:99669441-100406394	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv879654	chr4:99748988-99877402	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:99802800-99849000	Weak transcription	Aorta	Aorta
2	chr4:99804400-99848800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr4:99807200-99849000	Weak transcription	Colonic Mucosa	Colon
4	chr4:99808600-99849000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr4:99815800-99848200	Weak transcription	Stomach Smooth Muscle	stomach
6	chr4:99823000-99848800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr4:99823000-99849000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr4:99823000-99849200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr4:99823200-99848000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr4:99823200-99848600	Weak transcription	Fetal Muscle Leg	muscle
11	chr4:99823200-99848800	Weak transcription	Placenta	Placenta
12	chr4:99827000-99848200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr4:99830000-99848200	Weak transcription	Fetal Kidney	kidney
14	chr4:99831000-99849200	Weak transcription	Gastric	stomach
15	chr4:99831200-99848000	Weak transcription	Brain Germinal Matrix	brain
16	chr4:99831200-99848000	Weak transcription	Brain Hippocampus Middle	brain
17	chr4:99831400-99848800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr4:99832200-99848000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr4:99832200-99848000	Weak transcription	Duodenum Mucosa	Duodenum
20	chr4:99832200-99848000	Weak transcription	Fetal Stomach	stomach
21	chr4:99832200-99848000	Weak transcription	NHDF-Ad	bronchial
22	chr4:99832200-99848800	Weak transcription	Rectal Smooth Muscle	rectum
23	chr4:99832400-99849000	Weak transcription	Right Atrium	heart
24	chr4:99832600-99849200	Weak transcription	Spleen	Spleen
25	chr4:99836000-99848000	Weak transcription	Brain Anterior Caudate	brain
26	chr4:99837600-99848400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr4:99838200-99848400	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr4:99838400-99848000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr4:99838400-99848800	Weak transcription	Adipose Nuclei	Adipose
30	chr4:99838600-99848000	Weak transcription	Primary T cells from cord blood	blood
31	chr4:99838800-99848800	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr4:99838800-99848800	Weak transcription	Small Intestine	intestine
33	chr4:99839000-99849200	Weak transcription	Ovary	ovary
34	chr4:99839200-99848400	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr4:99839200-99849400	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr4:99839400-99849200	Weak transcription	Lung	lung
37	chr4:99840400-99848800	Weak transcription	HSMMtube	muscle
38	chr4:99841000-99849200	Weak transcription	Pancreas	Pancrea
39	chr4:99841600-99848000	Weak transcription	HSMM	muscle
40	chr4:99841600-99849200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr4:99841800-99848000	Weak transcription	Fetal Brain Female	brain
42	chr4:99841800-99848000	Weak transcription	Stomach Mucosa	stomach
43	chr4:99842000-99848000	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr4:99842000-99848000	Weak transcription	NHLF	lung
45	chr4:99842800-99848000	Weak transcription	Primary neutrophils fromperipheralblood	blood
46	chr4:99842800-99848200	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr4:99843200-99848000	Weak transcription	Colon Smooth Muscle	Colon
48	chr4:99843400-99848000	Weak transcription	Pancreatic Islets	Pancreatic Islet
49	chr4:99843400-99848800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr4:99844800-99848400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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