Variant report

Variant	rs9866935
Chromosome Location	chr3:196256173-196256174
allele	G/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	MYC	chr3:196255714-196256281	H1-hESC	embryonic stem cell:	n/a	chr3:196255768-196255778
2	CTCF	chr3:196256040-196256190	GM12875	blood:	n/a	n/a
3	MAX	chr3:196255355-196256294	H1-hESC	embryonic stem cell:	n/a	chr3:196255768-196255778
4	YY1	chr3:196255369-196256229	H1-hESC	embryonic stem cell:	n/a	chr3:196255696-196255710 chr3:196255805-196255819 chr3:196255701-196255710 chr3:196255808-196255822
5	POLR2A	chr3:196255260-196256196	GM12878	blood:	n/a	n/a
6	TFAP2C	chr3:196255522-196256211	Hela-S3	cervix:	n/a	n/a
7	MYC	chr3:196255487-196256202	K562	blood:	n/a	chr3:196255768-196255778
8	TCF12	chr3:196255330-196256181	ECC-1	luminal epithelium:	n/a	n/a
9	FOXM1	chr3:196255374-196256238	GM12878	blood:	n/a	n/a
10	YY1	chr3:196255414-196256211	ECC-1	luminal epithelium:	n/a	chr3:196255696-196255710 chr3:196255805-196255819 chr3:196255701-196255710 chr3:196255808-196255822
11	POLR2A	chr3:196255391-196256191	K562	blood:	n/a	n/a
12	MAX	chr3:196255359-196256357	ECC-1	luminal epithelium:	n/a	chr3:196255768-196255778
13	MYC	chr3:196255423-196256390	A549	lung:	n/a	chr3:196255768-196255778
14	MAX	chr3:196255337-196256392	A549	lung:	n/a	chr3:196255768-196255778
15	MYC	chr3:196255446-196256259	K562	blood:	n/a	chr3:196255768-196255778
16	MAZ	chr3:196255376-196256177	IMR90	lung:	n/a	chr3:196255768-196255778
17	POLR2A	chr3:196255366-196256180	GM12892	blood:	n/a	n/a
18	MAX	chr3:196255348-196256378	A549	lung:	n/a	chr3:196255768-196255778
19	FOXM1	chr3:196255343-196256378	GM12878	blood:	n/a	n/a
20	PML	chr3:196255325-196256354	GM12878	blood:	n/a	n/a
21	ZC3H11A	chr3:196255784-196256191	K562	blood:	n/a	n/a
22	MAX	chr3:196255352-196256367	H1-hESC	embryonic stem cell:	n/a	chr3:196255768-196255778
23	CTBP2	chr3:196255490-196256177	H1-hESC	embryonic stem cell:	n/a	n/a
24	E2F6	chr3:196255349-196256307	H1-hESC	embryonic stem cell:	n/a	n/a
25	MXI1	chr3:196255504-196256180	K562	blood:	n/a	n/a
26	POLR2A	chr3:196255322-196256217	HUVEC	blood vessel:	n/a	n/a
27	MTA3	chr3:196253937-196256337	GM12878	blood:	n/a	n/a
28	EP300	chr3:196255358-196256227	ECC-1	luminal epithelium:	n/a	chr3:196255771-196255780
29	MAX	chr3:196255425-196256209	K562	blood:	n/a	chr3:196255768-196255778
30	POLR2A	chr3:196255385-196256176	H1-hESC	embryonic stem cell:	n/a	n/a
31	RUNX3	chr3:196255340-196256297	GM12878	blood:	n/a	n/a
32	YY1	chr3:196255500-196256203	ECC-1	luminal epithelium:	n/a	chr3:196255696-196255710 chr3:196255805-196255819 chr3:196255701-196255710 chr3:196255808-196255822
33	REST	chr3:196255369-196256269	A549	lung:	n/a	chr3:196255753-196255763
34	TAF1	chr3:196255365-196256230	ECC-1	luminal epithelium:	n/a	n/a
35	MAX	chr3:196255389-196256252	A549	lung:	n/a	chr3:196255768-196255778
36	TAF1	chr3:196255386-196256302	ECC-1	luminal epithelium:	n/a	n/a
37	CTCF	chr3:196255381-196256287	SK-N-SH	brain:	n/a	chr3:196255804-196255814 chr3:196255801-196255822 chr3:196255799-196255817 chr3:196255802-196255811 chr3:196255802-196255815 chr3:196255800-196255816
38	RAD21	chr3:196255358-196256227	HCT-116	colon:	n/a	chr3:196255800-196255819 chr3:196255805-196255817 chr3:196255805-196255815 chr3:196255801-196255815 chr3:196255828-196255842
39	POLR2A	chr3:196255268-196256264	GM12892	blood:	n/a	n/a
40	NFIC	chr3:196255248-196256262	GM12878	blood:	n/a	n/a
41	USF1	chr3:196255455-196256263	ECC-1	luminal epithelium:	n/a	chr3:196255764-196255780 chr3:196255835-196255851
42	MAX	chr3:196255346-196256388	ECC-1	luminal epithelium:	n/a	chr3:196255768-196255778
43	YY1	chr3:196255485-196256213	GM12878	blood:	n/a	chr3:196255696-196255710 chr3:196255805-196255819 chr3:196255701-196255710 chr3:196255808-196255822
44	MAX	chr3:196255295-196256308	K562	blood:	n/a	chr3:196255768-196255778
45	YY1	chr3:196255419-196256173	GM12878	blood:	n/a	chr3:196255696-196255710 chr3:196255805-196255819 chr3:196255701-196255710 chr3:196255808-196255822
46	TCF12	chr3:196255352-196256216	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:196255847..196257386-chr3:196258042..196259736,2	K562	blood:
2	chr3:196256161..196258793-chr3:196292784..196296820,3	MCF-7	breast:
3	chr3:196255773..196256767-chr3:196411387..196411995,2	K562	blood:

Variant related genes	Relation type
ENSG00000213358	TF binding region
ENSG00000185798	Chromatin interaction
ENSG00000174013	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs2054747	1.00[ASN][1000 genomes]
rs6583312	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6583314	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6583315	1.00[ASN][1000 genomes]
rs6583316	0.93[AMR][1000 genomes]
rs6767712	1.00[ASN][1000 genomes]
rs6768682	0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6783108	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6786154	0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6807731	1.00[ASN][1000 genomes]
rs7374776	1.00[ASN][1000 genomes]
rs7615630	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7616415	1.00[ASN][1000 genomes]
rs7623203	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7625068	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7633212	1.00[ASN][1000 genomes]
rs7640505	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003194	chr3:195960270-196342423	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
2	nsv536894	chr3:195960270-196342423	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
3	nsv1003066	chr3:196098763-196414159	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats 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	55 gene(s)	inside rSNPs	diseases
4	esv2752687	chr3:196147690-196286690	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	nsv948681	chr3:196148055-197007546	Weak transcription Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
6	nsv1010483	chr3:196210054-196319543	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
7	nsv536896	chr3:196210054-196319543	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
8	nsv1014692	chr3:196242249-196531824	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
9	esv2763750	chr3:196242261-196278366	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
10	nsv878187	chr3:196245603-196554790	Enhancers ZNF genes & repeats Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
11	nsv967108	chr3:196255474-196263970	Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:196255000-196256200	Active TSS	A549	lung
2	chr3:196255200-196256200	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr3:196255200-196256200	Enhancers	Primary B cells from cord blood	blood
4	chr3:196255400-196256200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr3:196255400-196256200	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr3:196255400-196256200	Active TSS	HUES48 Cell Line	embryonic stem cell
7	chr3:196255400-196256200	Active TSS	HUES64 Cell Line	embryonic stem cell
8	chr3:196255400-196256200	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr3:196255400-196256200	Active TSS	iPS-20b Cell Line	embryonic stem cell
10	chr3:196255400-196256200	Active TSS	Breast Myoepithelial Primary Cells	Breast
11	chr3:196255400-196256200	Flanking Active TSS	Primary B cells from peripheral blood	blood
12	chr3:196255400-196256200	Active TSS	Primary T cells from cord blood	blood
13	chr3:196255400-196256200	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
14	chr3:196255400-196256200	Flanking Active TSS	Primary hematopoietic stem cells	blood
15	chr3:196255400-196256200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
16	chr3:196255400-196256200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
17	chr3:196255400-196256200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
18	chr3:196255400-196256200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
19	chr3:196255400-196256200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr3:196255400-196256200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr3:196255400-196256200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr3:196255400-196256200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr3:196255400-196256200	Active TSS	Brain Germinal Matrix	brain
24	chr3:196255400-196256200	Active TSS	Duodenum Mucosa	Duodenum
25	chr3:196255400-196256200	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
26	chr3:196255400-196256200	Active TSS	Fetal Intestine Large	intestine
27	chr3:196255400-196256200	Active TSS	Fetal Kidney	kidney
28	chr3:196255400-196256200	Flanking Active TSS	Fetal Muscle Trunk	muscle
29	chr3:196255400-196256200	Enhancers	Pancreas	Pancrea
30	chr3:196255400-196256200	Active TSS	Psoas Muscle	Psoas
31	chr3:196255400-196256200	Active TSS	Rectal Mucosa Donor 31	rectum
32	chr3:196255400-196256200	Active TSS	Rectal Smooth Muscle	rectum
33	chr3:196255400-196256200	Flanking Active TSS	Stomach Smooth Muscle	stomach
34	chr3:196255400-196256200	Flanking Active TSS	Thymus	Thymus
35	chr3:196255400-196256200	Enhancers	Spleen	Spleen
36	chr3:196255400-196256200	Flanking Active TSS	Dnd41	blood
37	chr3:196255400-196256200	Flanking Active TSS	Hela-S3	cervix
38	chr3:196255400-196256200	Active TSS	HSMM	muscle
39	chr3:196255400-196256200	Active TSS	NHDF-Ad	bronchial
40	chr3:196255400-196256400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr3:196255400-196256400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr3:196255400-196256400	Active TSS	Brain Inferior Temporal Lobe	brain
43	chr3:196255600-196256200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
44	chr3:196255600-196256200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
45	chr3:196255600-196256200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr3:196255600-196256200	Bivalent/Poised TSS	Brain Angular Gyrus	brain
47	chr3:196255600-196256200	Bivalent/Poised TSS	Fetal Stomach	stomach
48	chr3:196255600-196256200	Active TSS	Skeletal Muscle Male	skeletal muscle
49	chr3:196255600-196256200	Active TSS	NHLF	lung
50	chr3:196255600-196256400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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