Variant report

Variant	rs2602421
Chromosome Location	chr16:81039627-81039628
allele	A/G
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	TEAD4	chr16:81039232-81039678	H1-hESC	embryonic stem cell:	n/a	n/a
2	CHD1	chr16:81039496-81039954	H1-hESC	embryonic stem cell:	n/a	n/a
3	SIN3AK20	chr16:81039392-81041620	MCF-7	breast:	n/a	n/a
4	TBP	chr16:81039297-81041451	Hela-S3	cervix:	n/a	n/a
5	MAX	chr16:81039155-81041501	A549	lung:	n/a	chr16:81040795-81040805 chr16:81040695-81040704 chr16:81041155-81041164
6	POLR2A	chr16:81039052-81041720	H1-hESC	embryonic stem cell:	n/a	n/a
7	JUND	chr16:81039279-81042090	SK-N-SH	brain:	n/a	chr16:81041079-81041088
8	SIN3A	chr16:81039358-81041579	H1-hESC	embryonic stem cell:	n/a	chr16:81041064-81041077 chr16:81040175-81040188
9	SIN3AK20	chr16:81039313-81041611	HCT-116	colon:	n/a	n/a
10	IRF1	chr16:81039214-81041494	K562	blood:	n/a	chr16:81039570-81039584 chr16:81039573-81039587 chr16:81041214-81041225 chr16:81041214-81041226 chr16:81039575-81039591 chr16:81039572-81039585 chr16:81041214-81041226 chr16:81039572-81039586 chr16:81040780-81040794
11	MAX	chr16:81039205-81039664	Hela-S3	cervix:	n/a	n/a
12	MXI1	chr16:81039314-81041465	GM12878	blood:	n/a	n/a
13	CTCF	chr16:81039528-81039655	K562	blood:	n/a	n/a
14	POLR2A	chr16:81039134-81041558	Hela-S3	cervix:	n/a	n/a
15	JUN	chr16:81039044-81041495	K562	blood:	n/a	chr16:81041079-81041088 chr16:81041078-81041091
16	MXI1	chr16:81039306-81039642	HepG2	liver:	n/a	n/a
17	MXI1	chr16:81039145-81042276	SK-N-SH	brain:	n/a	n/a
18	MYC	chr16:81039339-81039836	MCF10A-Er-Src	breast:	n/a	n/a
19	SMARCC1	chr16:81039221-81041876	Hela-S3	cervix:	n/a	n/a
20	MAX	chr16:81039347-81041493	NB4	blood:	n/a	chr16:81040795-81040805 chr16:81040695-81040704 chr16:81041155-81041164
21	IRF1	chr16:81039242-81041462	K562	blood:	n/a	chr16:81039570-81039584 chr16:81039573-81039587 chr16:81041214-81041225 chr16:81041214-81041226 chr16:81039575-81039591 chr16:81039572-81039585 chr16:81041214-81041226 chr16:81039572-81039586 chr16:81040780-81040794
22	MYC	chr16:81039505-81039702	MCF10A-Er-Src	breast:	n/a	n/a
23	SIN3AK20	chr16:81039625-81041436	K562	blood:	n/a	n/a
24	POLR2A	chr16:81038829-81041850	Hela-S3	cervix:	n/a	n/a
25	HCFC1	chr16:81039075-81042051	Hela-S3	cervix:	n/a	n/a
26	MXI1	chr16:81039325-81039712	Hela-S3	cervix:	n/a	n/a
27	TEAD4	chr16:81039194-81040285	HepG2	liver:	n/a	n/a
28	MAX	chr16:81039205-81039688	K562	blood:	n/a	n/a
29	ZNF263	chr16:81039285-81041416	HEK293-T-REx	kidney:	n/a	n/a
30	POLR2A	chr16:81039405-81039684	GM12878	blood:	n/a	n/a
31	RUNX3	chr16:81039532-81041628	GM12878	blood:	n/a	n/a
32	CHD1	chr16:81039191-81042059	IMR90	lung:	n/a	chr16:81041086-81041096
33	E2F4	chr16:81039582-81041505	MCF10A-Er-Src	breast:	n/a	chr16:81040835-81040846 chr16:81040519-81040528 chr16:81041080-81041089 chr16:81040797-81040809 chr16:81040798-81040809 chr16:81041078-81041087

No.	Distal block	Cell Line	Cell type
1	chr16:81025473..81027772-chr16:81037035..81041311,4	K562	blood:
2	chr16:81038258..81040784-chr16:81347032..81349945,2	K562	blood:
3	chr16:81038105..81044923-chr16:81066300..81070952,14	MCF-7	breast:
4	chr16:81037151..81044642-chr16:81065528..81070966,16	K562	blood:
5	chr16:81028135..81034571-chr16:81035246..81044200,13	K562	blood:
6	chr16:81039624..81041255-chr16:81107979..81110813,2	MCF-7	breast:
7	chr16:81038653..81041025-chr16:81346635..81349129,2	MCF-7	breast:
8	chr16:81037996..81043724-chr16:81066407..81071400,11	MCF-7	breast:
9	chr16:81038376..81042418-chr16:81108432..81111584,4	K562	blood:
10	chr16:81037094..81043910-chr16:81050858..81058489,11	MCF-7	breast:
11	chr16:81039002..81041272-chr16:81057250..81059847,2	MCF-7	breast:
12	chr16:81038376..81043277-chr16:81108432..81112403,6	K562	blood:
13	chr16:81038922..81040878-chr16:81128552..81130305,2	MCF-7	breast:
14	chr16:81037151..81042784-chr16:81066438..81073797,14	K562	blood:
15	chr1:156051144..156052645-chr16:81039463..81041221,2	MCF-7	breast:
16	chr16:81036155..81041262-chr16:81074086..81079875,7	K562	blood:

Variant related genes	Relation type
CENPN	TF binding region
ENSG00000261609	Chromatin interaction
ENSG00000166455	Chromatin interaction
ENSG00000260495	Chromatin interaction
ENSG00000140905	Chromatin interaction
ENSG00000260213	Chromatin interaction
ENSG00000254726	Chromatin interaction
ENSG00000160789	Chromatin interaction
ENSG00000103121	Chromatin interaction
ENSG00000245059	Chromatin interaction
ENSG00000166454	Chromatin interaction
ENSG00000166451	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs1349755	1.00[AMR][1000 genomes]
rs1349756	0.88[AFR][1000 genomes]
rs2194320	1.00[AMR][1000 genomes]
rs2549876	1.00[AMR][1000 genomes]
rs2602420	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28430837	1.00[AMR][1000 genomes]
rs754428	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	nsv948534	chr16:80867635-81160492	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv1065258	chr16:80887483-81081768	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv1058045	chr16:80918138-81048242	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
4	nsv1064164	chr16:80918138-81126967	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
5	nsv542991	chr16:80918138-81126967	Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
6	nsv532569	chr16:80980356-81700149	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
7	nsv532597	chr16:81009718-81388348	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer 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	56 gene(s)	inside rSNPs	diseases
8	nsv573338	chr16:81020393-81106944	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
9	nsv427984	chr16:81026691-81320341	Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription 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	49 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2602421	GCSH	cis	lymphoblastoid	seeQTL
rs2602421	C16orf61	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:81037600-81039800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr16:81037600-81039800	Enhancers	Small Intestine	intestine
3	chr16:81037600-81040000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr16:81037800-81040000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr16:81037800-81040000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr16:81037800-81042000	Active TSS	Pancreatic Islets	Pancreatic Islet
7	chr16:81037800-81042400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr16:81038000-81039800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr16:81038000-81040000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
10	chr16:81038200-81041800	Active TSS	Ovary	ovary
11	chr16:81038200-81041800	Active TSS	Hela-S3	cervix
12	chr16:81038200-81042000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr16:81038200-81042400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr16:81038400-81042000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
15	chr16:81038400-81042200	Active TSS	ES-I3 Cell Line	embryonic stem cell
16	chr16:81038400-81042200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr16:81038600-81039800	Flanking Active TSS	NH-A	brain
18	chr16:81038600-81040000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
19	chr16:81038800-81039800	Enhancers	Spleen	Spleen
20	chr16:81038800-81041800	Active TSS	Left Ventricle	heart
21	chr16:81038800-81042000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr16:81038800-81042200	Active TSS	HUES48 Cell Line	embryonic stem cell
23	chr16:81038800-81042200	Active TSS	A549	lung
24	chr16:81038800-81042400	Active TSS	HUES64 Cell Line	embryonic stem cell
25	chr16:81039000-81039800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
26	chr16:81039000-81039800	Flanking Active TSS	Thymus	Thymus
27	chr16:81039000-81040000	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
28	chr16:81039200-81039800	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr16:81039200-81039800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr16:81039200-81039800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
31	chr16:81039200-81039800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
32	chr16:81039200-81039800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
33	chr16:81039200-81039800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
34	chr16:81039200-81039800	Flanking Active TSS	Brain Anterior Caudate	brain
35	chr16:81039200-81039800	Flanking Active TSS	Colon Smooth Muscle	Colon
36	chr16:81039200-81039800	Flanking Active TSS	Duodenum Mucosa	Duodenum
37	chr16:81039200-81039800	Flanking Active TSS	Fetal Kidney	kidney
38	chr16:81039200-81039800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
39	chr16:81039200-81039800	Flanking Active TSS	Rectal Smooth Muscle	rectum
40	chr16:81039200-81039800	Flanking Active TSS	HSMMtube	muscle
41	chr16:81039200-81039800	Flanking Active TSS	K562	blood
42	chr16:81039200-81039800	Flanking Active TSS	Osteobl	bone
43	chr16:81039200-81040000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr16:81039200-81040000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
45	chr16:81039200-81040000	Flanking Active TSS	Primary hematopoietic stem cells	blood
46	chr16:81039200-81040000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
47	chr16:81039200-81040000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
48	chr16:81039200-81040000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
49	chr16:81039200-81040000	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
50	chr16:81039200-81040000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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