Variant report

Variant	rs72934644
Chromosome Location	chr3:98527454-98527455
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	POLR2A	chr3:98523635-98529478	U87	brain:	n/a	n/a
2	POLR2A	chr3:98523592-98529440	U87	brain:	n/a	n/a
3	POLR2A	chr3:98523586-98529440	U87	brain:	n/a	n/a
4	POLR2A	chr3:98523621-98529478	U87	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:98310981..98313806-chr3:98526146..98529080,2	MCF-7	breast:

Variant related genes	Relation type
RNU6-26P	TF binding region
ENSG00000080819	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs13085453	1.00[AMR][1000 genomes]
rs56996908	1.00[AMR][1000 genomes]
rs57492353	1.00[AMR][1000 genomes]
rs57581846	1.00[AMR][1000 genomes]
rs58345395	1.00[AMR][1000 genomes]
rs58880987	1.00[AMR][1000 genomes]
rs58977425	1.00[AMR][1000 genomes]
rs58988785	1.00[AMR][1000 genomes]
rs59462320	1.00[AMR][1000 genomes]
rs59581962	1.00[AMR][1000 genomes]
rs59726038	1.00[AMR][1000 genomes]
rs60266120	1.00[AMR][1000 genomes]
rs60488063	1.00[AMR][1000 genomes]
rs61133181	1.00[AMR][1000 genomes]
rs61172524	1.00[AMR][1000 genomes]
rs61517408	1.00[AMR][1000 genomes]
rs72923005	1.00[AMR][1000 genomes]
rs72923016	1.00[AMR][1000 genomes]
rs72923020	1.00[AMR][1000 genomes]
rs72923040	1.00[AMR][1000 genomes]
rs72923043	1.00[AMR][1000 genomes]
rs72923045	1.00[AMR][1000 genomes]
rs72923046	1.00[AMR][1000 genomes]
rs72923053	1.00[AMR][1000 genomes]
rs72923071	1.00[AMR][1000 genomes]
rs72934627	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72934633	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72934639	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72934650	1.00[AMR][1000 genomes]
rs72934662	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72934664	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72934665	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72934681	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72934683	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72934691	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72936622	1.00[AMR][1000 genomes]
rs72936644	1.00[AMR][1000 genomes]
rs72936652	1.00[AMR][1000 genomes]
rs72936657	1.00[AMR][1000 genomes]
rs72936667	1.00[AMR][1000 genomes]
rs72936668	1.00[AMR][1000 genomes]
rs72938539	1.00[AMR][1000 genomes]
rs72938573	1.00[AMR][1000 genomes]
rs72938584	1.00[AMR][1000 genomes]
rs72938585	1.00[AMR][1000 genomes]
rs72940515	1.00[AMR][1000 genomes]
rs72940521	1.00[AMR][1000 genomes]
rs72940528	1.00[AMR][1000 genomes]
rs72940538	1.00[AMR][1000 genomes]
rs72940543	1.00[AMR][1000 genomes]
rs72940552	1.00[AMR][1000 genomes]
rs72940570	1.00[AMR][1000 genomes]
rs72940573	1.00[AMR][1000 genomes]
rs72940576	1.00[AMR][1000 genomes]
rs72940577	1.00[AMR][1000 genomes]
rs72940581	1.00[AMR][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	esv3390386	chr3:98174549-98579953	Genic enhancers Strong transcription Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv591065	chr3:98204198-98766326	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1007140	chr3:98421229-99202458	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv536663	chr3:98421229-99202458	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv877214	chr3:98445324-98738006	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
6	nsv1009032	chr3:98514221-98607721	Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98484800-98529800	Weak transcription	Primary B cells from cord blood	blood
2	chr3:98503400-98576400	Weak transcription	Gastric	stomach
3	chr3:98504600-98534800	Weak transcription	Small Intestine	intestine
4	chr3:98507800-98529000	Weak transcription	Brain Substantia Nigra	brain
5	chr3:98513600-98536600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr3:98513600-98539200	Weak transcription	Colonic Mucosa	Colon
7	chr3:98515600-98533400	Weak transcription	Fetal Intestine Small	intestine
8	chr3:98516800-98528600	Weak transcription	Primary hematopoietic stem cells	blood
9	chr3:98516800-98544000	Weak transcription	Spleen	Spleen
10	chr3:98517200-98531400	Weak transcription	Hela-S3	cervix
11	chr3:98520600-98528200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr3:98522400-98533800	Strong transcription	Muscle Satellite Cultured Cells	--
13	chr3:98523400-98531400	Strong transcription	HUES48 Cell Line	embryonic stem cell
14	chr3:98523600-98528200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr3:98523600-98528600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr3:98523600-98533800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr3:98523600-98535200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
18	chr3:98523800-98528200	Strong transcription	Duodenum Smooth Muscle	Duodenum
19	chr3:98523800-98528200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr3:98523800-98528200	Strong transcription	Fetal Intestine Large	intestine
21	chr3:98523800-98528200	Strong transcription	Left Ventricle	heart
22	chr3:98523800-98528400	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr3:98523800-98528400	Strong transcription	Fetal Muscle Leg	muscle
24	chr3:98523800-98529200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr3:98523800-98529200	Strong transcription	Fetal Muscle Trunk	muscle
26	chr3:98523800-98529200	Strong transcription	Rectal Mucosa Donor 29	rectum
27	chr3:98523800-98529400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr3:98523800-98529400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr3:98523800-98529600	Strong transcription	Fetal Lung	lung
30	chr3:98523800-98530000	Strong transcription	Cortex derived primary cultured neurospheres	brain
31	chr3:98523800-98530200	Strong transcription	Dnd41	blood
32	chr3:98523800-98530400	Strong transcription	H1 Cell Line	embryonic stem cell
33	chr3:98523800-98530400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr3:98523800-98530600	Strong transcription	HUVEC	blood vessel
35	chr3:98523800-98531400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr3:98523800-98531400	Strong transcription	HUES6 Cell Line	embryonic stem cell
37	chr3:98523800-98533600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr3:98523800-98533600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr3:98523800-98533800	Strong transcription	NHDF-Ad	bronchial
40	chr3:98523800-98535000	Strong transcription	HUES64 Cell Line	embryonic stem cell
41	chr3:98523800-98543800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr3:98524000-98543600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr3:98524200-98530400	Strong transcription	NHLF	lung
44	chr3:98524200-98544200	Strong transcription	HSMM	muscle
45	chr3:98524400-98528600	Strong transcription	HepG2	liver
46	chr3:98524800-98530400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr3:98525400-98529200	Genic enhancers	NH-A	brain
48	chr3:98525600-98528400	Genic enhancers	HMEC	breast
49	chr3:98525600-98552400	Weak transcription	Right Ventricle	heart
50	chr3:98526000-98528600	Genic enhancers	NHEK	skin

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