Variant report

Variant	rs16910644
Chromosome Location	chr9:2844261-2844262
allele	A/C
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	CHD2	chr9:2843963-2844480	HepG2	liver:	n/a	n/a
2	EGR1	chr9:2843955-2844411	K562	blood:	n/a	chr9:2844117-2844130
3	RELA	chr9:2843922-2844837	GM18505	blood:	n/a	n/a
4	HDAC2	chr9:2843949-2844454	HepG2	liver:	n/a	n/a
5	E2F6	chr9:2844134-2844449	K562	blood:	n/a	chr9:2844338-2844349 chr9:2844304-2844313 chr9:2844302-2844311
6	MAX	chr9:2843816-2845012	Hela-S3	cervix:	n/a	n/a
7	YY1	chr9:2843891-2844437	H1-hESC	embryonic stem cell:	n/a	n/a
8	YY1	chr9:2843786-2844593	GM12878	blood:	n/a	n/a
9	POLR2A	chr9:2843792-2844821	Hela-S3	cervix:	n/a	n/a
10	SIN3AK20	chr9:2843835-2844449	H1-hESC	embryonic stem cell:	n/a	n/a
11	GABPA	chr9:2843773-2844467	K562	blood:	n/a	chr9:2844098-2844105
12	PML	chr9:2843863-2844555	K562	blood:	n/a	n/a
13	HA-E2F1	chr9:2843717-2844478	MCF-7	breast:	n/a	chr9:2844304-2844313 chr9:2844302-2844311
14	POLR2A	chr9:2843857-2844526	GM12891	blood:	n/a	n/a
15	TAF1	chr9:2843776-2844640	GM12878	blood:	n/a	n/a
16	POLR2A	chr9:2843734-2845018	GM12892	blood:	n/a	n/a
17	CREB1	chr9:2843785-2844708	GM12878	blood:	n/a	chr9:2844301-2844314
18	SP1	chr9:2843865-2844533	GM12878	blood:	n/a	chr9:2844114-2844125 chr9:2844115-2844124 chr9:2844114-2844126 chr9:2844116-2844125 chr9:2844165-2844176 chr9:2844114-2844126
19	ELF1	chr9:2843848-2844495	HepG2	liver:	n/a	n/a
20	TCF7L2	chr9:2843863-2844491	HCT-116	colon:	n/a	n/a
21	SP1	chr9:2843827-2844481	H1-hESC	embryonic stem cell:	n/a	chr9:2844114-2844125 chr9:2844115-2844124 chr9:2844114-2844126 chr9:2844116-2844125 chr9:2844165-2844176 chr9:2844114-2844126
22	JUND	chr9:2843808-2844520	A549	lung:	n/a	chr9:2844303-2844312
23	POLR2A	chr9:2843792-2844530	A549	lung:	n/a	n/a
24	REST	chr9:2843883-2844477	PFSK-1	brain:	n/a	chr9:2843986-2843996
25	STAT3	chr9:2844058-2844704	GM12878	blood:	n/a	n/a
26	MYBL2	chr9:2843839-2844639	HepG2	liver:	n/a	n/a
27	EP300	chr9:2843937-2844564	GM12878	blood:	n/a	chr9:2844116-2844132
28	MAX	chr9:2843807-2844562	MCF-7	breast:	n/a	n/a
29	MYC	chr9:2843781-2844704	A549	lung:	n/a	n/a
30	FOSL2	chr9:2843865-2844576	A549	lung:	n/a	chr9:2844303-2844312
31	CREB1	chr9:2843881-2844703	H1-hESC	embryonic stem cell:	n/a	chr9:2844301-2844314
32	FOS	chr9:2844029-2844457	MCF10A-Er-Src	breast:	n/a	chr9:2844303-2844312
33	MYC	chr9:2843945-2844345	Hela-S3	cervix:	n/a	n/a
34	ATF3	chr9:2844110-2844452	K562	blood:	n/a	chr9:2844300-2844315 chr9:2844304-2844312 chr9:2844292-2844312 chr9:2844303-2844311 chr9:2844304-2844311
35	EP300	chr9:2843947-2844490	GM12878	blood:	n/a	chr9:2844116-2844132
36	POLR2A	chr9:2843907-2844592	PANC-1	pancreas:	n/a	n/a
37	YY1	chr9:2843779-2844522	GM12892	blood:	n/a	n/a
38	SRF	chr9:2843907-2844535	H1-hESC	embryonic stem cell:	n/a	n/a
39	RCOR1	chr9:2843930-2844494	K562	blood:	n/a	n/a
40	JUN	chr9:2843782-2844697	K562	blood:	n/a	chr9:2844299-2844312 chr9:2844303-2844312
41	HEY1	chr9:2843785-2844583	K562	blood:	n/a	chr9:2844115-2844130
42	HDAC2	chr9:2843867-2844423	H1-hESC	embryonic stem cell:	n/a	n/a
43	SRF	chr9:2843872-2844778	HCT-116	colon:	n/a	n/a
44	EP300	chr9:2843852-2844623	A549	lung:	n/a	chr9:2844116-2844132
45	YY1	chr9:2843891-2844532	SK-N-SH_RA	brain:	n/a	n/a
46	E2F4	chr9:2843982-2844525	MCF10A-Er-Src	breast:	n/a	chr9:2844304-2844313 chr9:2844302-2844311
47	POLR2A	chr9:2843788-2844572	K562	blood:	n/a	n/a
48	POLR2A	chr9:2843842-2844577	HEK293	kidney:	n/a	n/a
49	MYC	chr9:2843839-2844546	K562	blood:	n/a	n/a
50	TBL1XR1	chr9:2844001-2844539	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:100209591..100210113-chr9:2844054..2844824,2	NB4	blood:
2	chr9:2806397..2808732-chr9:2841740..2844486,2	MCF-7	breast:
3	chr9:2841657..2846061-chr9:3525153..3529600,6	K562	blood:
4	chr9:2842064..2844768-chr9:3524803..3527756,2	K562	blood:
5	chr6:159070944..159071444-chr9:2843948..2844807,2	NB4	blood:

Variant related genes	Relation type
KIAA0020	TF binding region
ENSG00000232104	Chromatin interaction
ENSG00000106330	Chromatin interaction
ENSG00000164674	Chromatin interaction
ENSG00000080298	Chromatin interaction
ENSG00000080608	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10120832	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs10967690	1.00[CEU][hapmap]
rs10968241	1.00[CEU][hapmap]
rs12001445	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs12683812	1.00[JPT][hapmap]
rs16910647	1.00[EUR][1000 genomes]
rs16910670	1.00[EUR][1000 genomes]
rs7848733	1.00[CEU][hapmap]

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	nsv530929	chr9:1998911-2925112	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv1017581	chr9:2494815-3172020	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv539934	chr9:2494815-3172020	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv892079	chr9:2681430-2931341	Weak transcription Enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv892081	chr9:2691186-2851026	Active TSS Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
6	nsv1024262	chr9:2703159-3067931	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	nsv1028011	chr9:2759097-2904277	Enhancers Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
8	nsv1022873	chr9:2768825-2863264	Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
9	nsv892083	chr9:2809548-2900651	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 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	chr9:2841800-2844800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr9:2842000-2844800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr9:2842400-2844800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr9:2842600-2844600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
5	chr9:2842600-2845400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr9:2842800-2844600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr9:2842800-2844600	Active TSS	Rectal Mucosa Donor 29	rectum
8	chr9:2842800-2844800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr9:2842800-2844800	Active TSS	Aorta	Aorta
10	chr9:2842800-2845000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr9:2842800-2845200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr9:2842800-2845200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr9:2842800-2845400	Active TSS	ES-I3 Cell Line	embryonic stem cell
14	chr9:2842800-2845400	Active TSS	H1 Cell Line	embryonic stem cell
15	chr9:2842800-2845400	Active TSS	K562	blood
16	chr9:2842800-2845600	Active TSS	Colonic Mucosa	Colon
17	chr9:2843000-2844600	Active TSS	iPS-18 Cell Line	embryonic stem cell
18	chr9:2843000-2844600	Active TSS	Fetal Adrenal Gland	Adrenal Gland
19	chr9:2843000-2844800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
20	chr9:2843000-2844800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr9:2843000-2844800	Active TSS	HUES64 Cell Line	embryonic stem cell
22	chr9:2843000-2844800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr9:2843000-2844800	Active TSS	Ovary	ovary
24	chr9:2843000-2844800	Active TSS	Right Ventricle	heart
25	chr9:2843000-2844800	Active TSS	HSMM	muscle
26	chr9:2843000-2844800	Active TSS	NH-A	brain
27	chr9:2843000-2845000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr9:2843000-2845000	Active TSS	Breast Myoepithelial Primary Cells	Breast
29	chr9:2843000-2845000	Active TSS	NHDF-Ad	bronchial
30	chr9:2843000-2845000	Active TSS	NHLF	lung
31	chr9:2843000-2845200	Active TSS	H9 Cell Line	embryonic stem cell
32	chr9:2843000-2845200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr9:2843000-2845200	Active TSS	Muscle Satellite Cultured Cells	--
34	chr9:2843000-2845200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr9:2843000-2845200	Active TSS	A549	lung
36	chr9:2843000-2845200	Active TSS	GM12878-XiMat	blood
37	chr9:2843000-2845400	Active TSS	HUES48 Cell Line	embryonic stem cell
38	chr9:2843000-2845400	Active TSS	HUES6 Cell Line	embryonic stem cell
39	chr9:2843000-2845400	Active TSS	Fetal Muscle Trunk	muscle
40	chr9:2843000-2845600	Active TSS	iPS-15b Cell Line	embryonic stem cell
41	chr9:2843000-2845600	Active TSS	Right Atrium	heart
42	chr9:2843200-2844600	Active TSS	Primary T helper cells PMA-I stimulated	--
43	chr9:2843200-2844600	Active TSS	Pancreatic Islets	Pancreatic Islet
44	chr9:2843200-2844600	Active TSS	HUVEC	blood vessel
45	chr9:2843200-2844800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr9:2843200-2844800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr9:2843200-2844800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr9:2843200-2844800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr9:2843200-2844800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr9:2843200-2844800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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