Variant report

Variant	rs9830672
Chromosome Location	chr3:53915459-53915460
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	MXI1	chr3:53914153-53917137	SK-N-SH	brain:	n/a	n/a
2	YY1	chr3:53915315-53916620	SK-N-SH	brain:	n/a	chr3:53916222-53916242 chr3:53916301-53916310
3	MAZ	chr3:53915007-53917351	IMR90	lung:	n/a	chr3:53915928-53915938
4	TAF1	chr3:53915416-53916456	H1-neurons	neurons:	n/a	n/a
5	MXI1	chr3:53914895-53916494	IMR90	lung:	n/a	n/a
6	POLR2A	chr3:53914925-53916520	GM19099	blood:	n/a	n/a
7	POLR2A	chr3:53914545-53916766	HepG2	liver:	n/a	n/a
8	POLR2A	chr3:53915158-53917310	MCF10A-Er-Src	breast:	n/a	n/a
9	HCFC1	chr3:53915035-53917009	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr3:53915217-53917615	MCF10A-Er-Src	breast:	n/a	n/a
11	POLR2A	chr3:53914423-53917935	GM12891	blood:	n/a	n/a
12	POLR2A	chr3:53914613-53918608	IMR90	lung:	n/a	n/a
13	POLR2A	chr3:53914533-53917912	GM12878	blood:	n/a	n/a
14	POLR2A	chr3:53915164-53916311	K562	blood:	n/a	n/a
15	YY1	chr3:53915373-53916574	H1-hESC	embryonic stem cell:	n/a	chr3:53916222-53916242 chr3:53916301-53916310
16	POLR2A	chr3:53915448-53918024	GM12892	blood:	n/a	n/a
17	POLR2A	chr3:53915455-53916510	U87	brain:	n/a	n/a
18	YY1	chr3:53915301-53916694	SK-N-SH	brain:	n/a	chr3:53916222-53916242 chr3:53916301-53916310
19	POLR2A	chr3:53915386-53916641	SK-N-MC	brain:	n/a	n/a
20	BRCA1	chr3:53915112-53915517	H1-hESC	embryonic stem cell:	n/a	n/a
21	POLR2A	chr3:53914664-53917943	GM12878	blood:	n/a	n/a
22	POLR2A	chr3:53914823-53916702	HUVEC	blood vessel:	n/a	n/a
23	POLR2A	chr3:53914395-53916554	H1-hESC	embryonic stem cell:	n/a	n/a
24	POLR2A	chr3:53914433-53916660	GM12892	blood:	n/a	n/a
25	REST	chr3:53914969-53916751	H1-neurons	neurons:	n/a	chr3:53915821-53915834 chr3:53915393-53915406
26	TAF1	chr3:53915441-53916484	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:53908420..53912131-chr3:53913956..53917012,3	MCF-7	breast:
2	chr3:53913333..53919757-chr3:53920203..53928086,26	K562	blood:
3	chr3:53906924..53910795-chr3:53914021..53916121,3	MCF-7	breast:
4	chr3:53914775..53921125-chr3:53923203..53927129,12	MCF-7	breast:
5	chr3:53915297..53916473-chr3:53925441..53926286,3	MCF-7	breast:
6	chr3:53913820..53918433-chr3:53924406..53927799,6	MCF-7	breast:
7	chr3:53901391..53905529-chr3:53913413..53917026,5	MCF-7	breast:
8	chr3:53880225..53881825-chr3:53914407..53917091,2	MCF-7	breast:

Variant related genes	Relation type
ACTR8	TF binding region
ENSG00000113811	Chromatin interaction
ENSG00000113812	Chromatin interaction
ENSG00000016391	Chromatin interaction
ENSG00000056736	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs11130383	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11130384	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11562	0.83[AFR][1000 genomes]
rs12715465	1.00[AMR][1000 genomes]
rs13321898	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13322337	1.00[AMR][1000 genomes]
rs13434145	1.00[AMR][1000 genomes]
rs28409957	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6782007	1.00[AMR][1000 genomes]
rs6785238	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6802878	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72556356	1.00[AMR][1000 genomes]
rs7614233	1.00[AMR][1000 genomes]
rs7636496	1.00[AMR][1000 genomes]
rs7637908	1.00[AMR][1000 genomes]
rs7640840	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9814675	1.00[AMR][1000 genomes]
rs9816010	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9818571	1.00[AMR][1000 genomes]
rs9823141	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9833359	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9834168	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9835258	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9849610	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9852243	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9859937	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9860224	1.00[AMR][1000 genomes]
rs9872403	1.00[AMR][1000 genomes]
rs9878250	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9882134	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003621	chr3:53448934-54425322	Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv1001128	chr3:53659570-53927842	Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1013783	chr3:53694418-53934781	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv876804	chr3:53833509-53934171	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	nsv1010575	chr3:53846741-53934781	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
6	nsv1006990	chr3:53849510-54285212	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
7	nsv997771	chr3:53852695-53926635	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
8	nsv1002141	chr3:53858541-53934781	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
9	nsv1014752	chr3:53912429-54123246	Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53914600-53915600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr3:53914600-53915600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
3	chr3:53914600-53915600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr3:53914600-53915600	Flanking Active TSS	Brain Angular Gyrus	brain
5	chr3:53914600-53915600	Flanking Active TSS	Brain Germinal Matrix	brain
6	chr3:53914600-53915600	Flanking Active TSS	Duodenum Mucosa	Duodenum
7	chr3:53914600-53915600	Enhancers	Spleen	Spleen
8	chr3:53914600-53915800	Flanking Active TSS	Adipose Nuclei	Adipose
9	chr3:53914800-53915600	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr3:53914800-53915600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
11	chr3:53914800-53915600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
12	chr3:53914800-53915600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
13	chr3:53914800-53915600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
14	chr3:53914800-53915600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
15	chr3:53914800-53915600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
16	chr3:53914800-53915600	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
17	chr3:53914800-53915600	Flanking Active TSS	Stomach Smooth Muscle	stomach
18	chr3:53914800-53915800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr3:53914800-53915800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
20	chr3:53914800-53916600	Active TSS	Fetal Muscle Trunk	muscle
21	chr3:53915000-53915600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
22	chr3:53915000-53915600	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
23	chr3:53915000-53915800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
24	chr3:53915000-53915800	Flanking Active TSS	Primary T cells from cord blood	blood
25	chr3:53915000-53915800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
26	chr3:53915000-53915800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr3:53915000-53916000	Flanking Active TSS	Primary B cells from cord blood	blood
28	chr3:53915000-53916800	Active TSS	HUES64 Cell Line	embryonic stem cell
29	chr3:53915200-53915600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
30	chr3:53915200-53915600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr3:53915200-53915600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr3:53915200-53915600	Flanking Active TSS	Liver	Liver
33	chr3:53915200-53915800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
34	chr3:53915200-53915800	Flanking Active TSS	Primary hematopoietic stem cells	blood
35	chr3:53915200-53915800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
36	chr3:53915200-53915800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr3:53915200-53916200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
38	chr3:53915200-53916400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr3:53915200-53916400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
40	chr3:53915200-53916400	Active TSS	Psoas Muscle	Psoas
41	chr3:53915200-53916600	Active TSS	ES-I3 Cell Line	embryonic stem cell
42	chr3:53915200-53916600	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr3:53915200-53916600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr3:53915200-53916600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr3:53915200-53916600	Active TSS	Breast Myoepithelial Primary Cells	Breast
46	chr3:53915200-53916600	Active TSS	Aorta	Aorta
47	chr3:53915200-53916600	Active TSS	Fetal Intestine Small	intestine
48	chr3:53915200-53916600	Active TSS	Left Ventricle	heart
49	chr3:53915200-53916600	Active TSS	Lung	lung
50	chr3:53915200-53916600	Active TSS	Pancreas	Pancrea

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