Variant report

Variant	rs73929087
Chromosome Location	chr2:38831107-38831108
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	RAD21	chr2:38830383-38831116	A549	lung:	n/a	n/a
2	SIN3AK20	chr2:38828533-38831144	MCF-7	breast:	n/a	n/a
3	CTCF	chr2:38831100-38831250	NHLF	lung:	n/a	n/a
4	CTCF	chr2:38831060-38831210	GM12865	blood:	n/a	n/a
5	WRNIP1	chr2:38830637-38831292	GM12878	blood:	n/a	n/a
6	TCF12	chr2:38828537-38831166	A549	lung:	n/a	n/a
7	RAD21	chr2:38827547-38831481	SK-N-SH	brain:	n/a	n/a
8	MYC	chr2:38829746-38831273	K562	blood:	n/a	n/a
9	IRF1	chr2:38829715-38831328	K562	blood:	n/a	chr2:38830259-38830268
10	TBL1XR1	chr2:38829976-38831144	K562	blood:	n/a	n/a
11	MTA3	chr2:38829795-38831382	GM12878	blood:	n/a	n/a
12	REST	chr2:38828498-38831160	H1-neurons	neurons:	n/a	chr2:38830014-38830027 chr2:38829373-38829386 chr2:38830026-38830039 chr2:38829806-38829819
13	MXI1	chr2:38829910-38831248	K562	blood:	n/a	n/a
14	CTCF	chr2:38829160-38831342	SK-N-SH	brain:	n/a	chr2:38830289-38830302 chr2:38830180-38830193
15	GTF3C2	chr2:38830085-38831215	Hela-S3	cervix:	n/a	n/a
16	MYBL2	chr2:38829479-38831296	HepG2	liver:	n/a	n/a
17	SIN3A	chr2:38828520-38831200	H1-hESC	embryonic stem cell:	n/a	chr2:38830115-38830126 chr2:38829851-38829864
18	CTCF	chr2:38829389-38831587	A549	lung:	n/a	chr2:38830289-38830302 chr2:38830180-38830193
19	TEAD4	chr2:38829192-38831120	K562	blood:	n/a	n/a
20	CHD1	chr2:38827485-38831648	IMR90	lung:	n/a	n/a
21	SMC3	chr2:38827460-38831532	SK-N-SH	brain:	n/a	chr2:38830755-38830765 chr2:38830289-38830299
22	POLR2A	chr2:38821640-38832164	K562	blood:	n/a	n/a
23	TEAD4	chr2:38830305-38831128	HepG2	liver:	n/a	n/a
24	BRCA1	chr2:38829969-38831123	Hela-S3	cervix:	n/a	n/a
25	RAD21	chr2:38830471-38831122	MCF-7	breast:	n/a	n/a
26	NRF1	chr2:38829810-38831204	SK-N-SH	brain:	n/a	n/a
27	HCFC1	chr2:38828046-38831217	Hela-S3	cervix:	n/a	n/a
28	ZNF143	chr2:38829895-38831314	K562	blood:	n/a	n/a
29	RCOR1	chr2:38829567-38831220	K562	blood:	n/a	n/a
30	POLR2A	chr2:38830464-38831386	HL-60	blood:	n/a	n/a
31	UBTF	chr2:38827334-38831119	K562	blood:	n/a	n/a
32	SMC3	chr2:38830416-38831118	HepG2	liver:	n/a	chr2:38830755-38830765
33	JUN	chr2:38829850-38831483	K562	blood:	n/a	chr2:38830257-38830266
34	CTCF	chr2:38831060-38831210	HPAF	blood vessel:	n/a	n/a
35	SIX5	chr2:38830154-38831173	A549	lung:	n/a	n/a
36	BHLHE40	chr2:38829838-38831429	K562	blood:	n/a	chr2:38829847-38829863 chr2:38830178-38830194
37	ZMIZ1	chr2:38829569-38831137	K562	blood:	n/a	n/a
38	NR2F2	chr2:38829773-38831415	K562	blood:	n/a	n/a
39	MYBL2	chr2:38829712-38831312	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:38828577..38831705-chr2:38976861..38979916,6	MCF-7	breast:
2	chr2:38825670..38832919-chr2:38891527..38903424,21	K562	blood:
3	chr2:38819128..38833161-chr2:38974716..38980003,37	K562	blood:
4	chr2:38823060..38827854-chr2:38827983..38831423,11	MCF-7	breast:
5	chr2:38824811..38832919-chr2:38891494..38898299,16	K562	blood:
6	chr2:38824074..38831950-chr2:38975822..38980618,12	MCF-7	breast:
7	chr2:38816516..38836019-chr2:38963690..38980163,62	K562	blood:
8	chr2:38830892..38832834-chr2:38919143..38921497,2	K562	blood:
9	chr2:38829496..38831232-chr2:38893143..38894875,2	MCF-7	breast:

Variant related genes	Relation type
HNRNPLL	TF binding region
ENSG00000143891	Chromatin interaction
ENSG00000232518	Chromatin interaction
ENSG00000152147	Chromatin interaction
ENSG00000143889	Chromatin interaction
ENSG00000115875	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs55773228	0.83[AFR][1000 genomes]
rs55820712	0.91[AFR][1000 genomes]
rs6732384	0.83[AMR][1000 genomes]
rs73929059	0.83[AMR][1000 genomes]
rs73929077	0.87[AFR][1000 genomes]
rs73931606	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7579589	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7594264	0.88[AFR][1000 genomes];0.83[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	nsv916059	chr2:38332341-39119398	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	143 gene(s)	inside rSNPs	diseases
2	nsv9646	chr2:38358311-39082189	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	141 gene(s)	inside rSNPs	diseases
3	nsv873881	chr2:38745624-38877636	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
4	nsv581482	chr2:38799820-38858669	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv581483	chr2:38799820-38862223	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers 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	17 gene(s)	inside rSNPs	diseases
6	nsv581484	chr2:38799820-38874177	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Strong transcription 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	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:38826400-38831400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr2:38827000-38831400	Active TSS	Duodenum Smooth Muscle	Duodenum
3	chr2:38827200-38831200	Active TSS	Brain Germinal Matrix	brain
4	chr2:38827400-38831200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr2:38827600-38831400	Active TSS	Colonic Mucosa	Colon
6	chr2:38828000-38831200	Active TSS	Psoas Muscle	Psoas
7	chr2:38828000-38831200	Active TSS	Rectal Mucosa Donor 31	rectum
8	chr2:38828000-38831400	Active TSS	Fetal Muscle Trunk	muscle
9	chr2:38828400-38831200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
10	chr2:38828800-38831400	Active TSS	Rectal Mucosa Donor 29	rectum
11	chr2:38829200-38831200	Active TSS	Liver	Liver
12	chr2:38829800-38831200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr2:38830400-38831200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
14	chr2:38830400-38831200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
15	chr2:38830400-38831200	Flanking Active TSS	GM12878-XiMat	blood
16	chr2:38830400-38831400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
17	chr2:38830400-38831400	Flanking Active TSS	Dnd41	blood
18	chr2:38830600-38831200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
19	chr2:38830600-38831200	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
20	chr2:38830600-38831200	Weak transcription	Lung	lung
21	chr2:38830600-38831200	Flanking Active TSS	Hela-S3	cervix
22	chr2:38830600-38831400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
23	chr2:38830600-38831400	Flanking Bivalent TSS/Enh	Primary B cells from cord blood	blood
24	chr2:38830600-38831400	Flanking Active TSS	K562	blood
25	chr2:38830600-38831600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
26	chr2:38830600-38832800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr2:38830800-38831200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
28	chr2:38830800-38831200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr2:38830800-38831200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr2:38830800-38831200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr2:38830800-38831200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr2:38830800-38831200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr2:38830800-38831200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr2:38830800-38831200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
35	chr2:38830800-38831200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
36	chr2:38830800-38831200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
37	chr2:38830800-38831200	Flanking Active TSS	Fetal Brain Male	brain
38	chr2:38830800-38831200	Enhancers	Fetal Heart	heart
39	chr2:38830800-38831200	Flanking Active TSS	Fetal Muscle Leg	muscle
40	chr2:38830800-38831200	Enhancers	Placenta Amnion	Placenta Amnion
41	chr2:38830800-38831200	Flanking Active TSS	Stomach Smooth Muscle	stomach
42	chr2:38830800-38831200	Flanking Active TSS	A549	lung
43	chr2:38830800-38831400	Enhancers	H9 Cell Line	embryonic stem cell
44	chr2:38830800-38831400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr2:38830800-38831400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
46	chr2:38830800-38831400	Enhancers	iPS-15b Cell Line	embryonic stem cell
47	chr2:38830800-38831400	Bivalent Enhancer	Primary B cells from peripheral blood	blood
48	chr2:38830800-38831400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
49	chr2:38830800-38831400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
50	chr2:38830800-38831400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood

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