Variant report

Variant	rs73955784
Chromosome Location	chr2:133429170-133429171
allele	A/C/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	NR2F2	chr2:133428937-133429456	MCF-7	breast:	n/a	n/a
2	MAX	chr2:133426800-133429516	A549	lung:	n/a	chr2:133429294-133429305 chr2:133427838-133427857 chr2:133427843-133427852 chr2:133427843-133427852 chr2:133428962-133428972
3	POLR2A	chr2:133426781-133429482	H1-neurons	neurons:	n/a	n/a
4	JUND	chr2:133429060-133429333	H1-hESC	embryonic stem cell:	n/a	chr2:133429300-133429311 chr2:133429301-133429310 chr2:133429303-133429310 chr2:133429298-133429309
5	POLR2A	chr2:133428252-133429367	HUVEC	blood vessel:	n/a	n/a
6	FOXA2	chr2:133428941-133429425	A549	lung:	n/a	n/a
7	TCF12	chr2:133428819-133429548	SK-N-SH	brain:	n/a	n/a
8	SIN3AK20	chr2:133426720-133429555	MCF-7	breast:	n/a	n/a
9	RAD21	chr2:133429046-133429370	SK-N-SH_RA	brain:	n/a	n/a
10	TEAD4	chr2:133428926-133429485	ECC-1	luminal epithelium:	n/a	n/a
11	NFIC	chr2:133428918-133429550	SK-N-SH	brain:	n/a	n/a
12	USF2	chr2:133429170-133429432	Hela-S3	cervix:	n/a	n/a
13	FOXA1	chr2:133429089-133429313	ECC-1	luminal epithelium:	n/a	n/a
14	CHD2	chr2:133429151-133429365	Hela-S3	cervix:	n/a	n/a
15	TCF12	chr2:133428903-133429608	ECC-1	luminal epithelium:	n/a	n/a
16	FOS	chr2:133428821-133429499	HUVEC	blood vessel:	n/a	chr2:133429300-133429311 chr2:133429300-133429311 chr2:133429301-133429310 chr2:133429303-133429310 chr2:133429298-133429309
17	EP300	chr2:133428920-133429556	A549	lung:	n/a	chr2:133429144-133429158 chr2:133429301-133429310
18	JUND	chr2:133428979-133429406	A549	lung:	n/a	chr2:133429300-133429311 chr2:133429301-133429310 chr2:133429303-133429310 chr2:133429298-133429309
19	MYC	chr2:133429147-133429445	MCF10A-Er-Src	breast:	n/a	chr2:133429294-133429305
20	FOS	chr2:133429037-133429488	MCF10A-Er-Src	breast:	n/a	chr2:133429300-133429311 chr2:133429300-133429311 chr2:133429301-133429310 chr2:133429303-133429310 chr2:133429298-133429309
21	RCOR1	chr2:133426142-133429474	IMR90	lung:	n/a	n/a
22	EP300	chr2:133429000-133429405	ECC-1	luminal epithelium:	n/a	chr2:133429144-133429158 chr2:133429301-133429310
23	MAX	chr2:133428774-133429409	SK-N-SH	brain:	n/a	chr2:133429294-133429305 chr2:133428962-133428972
24	JUN	chr2:133429132-133429463	HUVEC	blood vessel:	n/a	chr2:133429300-133429311 chr2:133429301-133429310 chr2:133429303-133429310 chr2:133429298-133429309
25	FOSL2	chr2:133428942-133429615	SK-N-SH	brain:	n/a	chr2:133429300-133429311 chr2:133429301-133429310 chr2:133429303-133429310 chr2:133429298-133429309
26	FOSL2	chr2:133428917-133429544	MCF-7	breast:	n/a	chr2:133429300-133429311 chr2:133429301-133429310 chr2:133429303-133429310 chr2:133429298-133429309
27	GATA2	chr2:133428839-133429457	HUVEC	blood vessel:	n/a	chr2:133429300-133429309
28	STAT3	chr2:133429033-133429495	MCF10A-Er-Src	breast:	n/a	chr2:133429275-133429283 chr2:133429273-133429284
29	CEBPB	chr2:133429137-133429391	IMR90	lung:	n/a	chr2:133429153-133429165
30	TBP	chr2:133429159-133429389	Hela-S3	cervix:	n/a	n/a
31	TEAD4	chr2:133428928-133429435	ECC-1	luminal epithelium:	n/a	n/a
32	TCF12	chr2:133428564-133429635	SK-N-SH	brain:	n/a	n/a
33	JUN	chr2:133429105-133429446	Hela-S3	cervix:	n/a	chr2:133429300-133429311 chr2:133429301-133429310 chr2:133429303-133429310 chr2:133429298-133429309
34	TCF7L2	chr2:133429069-133429303	MCF-7	breast:	n/a	n/a
35	SMC3	chr2:133429141-133429353	Hela-S3	cervix:	n/a	n/a
36	JUND	chr2:133429039-133429400	H1-hESC	embryonic stem cell:	n/a	chr2:133429300-133429311 chr2:133429301-133429310 chr2:133429303-133429310 chr2:133429298-133429309
37	STAT3	chr2:133429149-133429665	MCF10A-Er-Src	breast:	n/a	chr2:133429275-133429283 chr2:133429273-133429284
38	USF1	chr2:133429157-133429336	SK-N-SH_RA	brain:	n/a	n/a
39	STAT3	chr2:133429106-133429462	Hela-S3	cervix:	n/a	chr2:133429275-133429283 chr2:133429273-133429284
40	RAD21	chr2:133429104-133429427	Hela-S3	cervix:	n/a	n/a
41	TCF7L2	chr2:133429156-133429261	Hela-S3	cervix:	n/a	n/a
42	RFX5	chr2:133429084-133429470	Hela-S3	cervix:	n/a	n/a
43	TCF12	chr2:133428927-133429484	A549	lung:	n/a	n/a
44	EP300	chr2:133428979-133429409	SK-N-SH_RA	brain:	n/a	chr2:133429144-133429158 chr2:133429301-133429310
45	FOS	chr2:133429034-133429485	MCF10A-Er-Src	breast:	n/a	chr2:133429300-133429311 chr2:133429300-133429311 chr2:133429301-133429310 chr2:133429303-133429310 chr2:133429298-133429309
46	STAT3	chr2:133429072-133429599	MCF10A-Er-Src	breast:	n/a	chr2:133429275-133429283 chr2:133429273-133429284
47	MXI1	chr2:133429143-133429410	Hela-S3	cervix:	n/a	n/a
48	FOSL2	chr2:133428912-133429499	A549	lung:	n/a	chr2:133429300-133429311 chr2:133429301-133429310 chr2:133429303-133429310 chr2:133429298-133429309
49	PBX3	chr2:133428959-133429450	SK-N-SH	brain:	n/a	n/a
50	FOS	chr2:133429015-133429562	MCF10A-Er-Src	breast:	n/a	chr2:133429300-133429311 chr2:133429300-133429311 chr2:133429301-133429310 chr2:133429303-133429310 chr2:133429298-133429309

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr2:133429169-133429219	AG04449	skin:	fetal
2	chr2:133429169-133429219	H1-hESC	embryonic stem cell:	embryo
3	chr2:133429169-133429219	PANC-1	pancreas:	n/a
4	chr2:133429169-133429219	AG10803	skin:	n/a
5	chr2:133429169-133429219	HPAEpiC	pulmonary alveolar:	n/a
6	chr2:133429169-133429219	GM19239	blood:	n/a
7	chr2:133429169-133429219	ProgFib	skin:	n/a
8	chr2:133429169-133429219	HEEpiC	esophagus:	n/a
9	chr2:133429169-133429219	NB4	blood:	n/a
10	chr2:133429169-133429219	LNCaP	prostate:	n/a
11	chr2:133429169-133429219	HIPEpiC	eye:	n/a
12	chr2:133429169-133429219	HRE	kidney:	n/a
13	chr2:133429169-133429219	CMK	blood:	n/a
14	chr2:133429169-133429219	NHBE	bronchial:	n/a
15	chr2:133429169-133429219	MCF-7	breast:	n/a
16	chr2:133429169-133429219	MCF10A-Er-Src	breast:	n/a
17	chr2:133429169-133429219	SAEC	small airway:	n/a
18	chr2:133429169-133429219	Hepatocyte	liver:	n/a
19	chr2:133429169-133429219	HCPEpiC	choroid plexus:	n/a
20	chr2:133429169-133429219	HEK293	kidney:	embryo
21	chr2:133429169-133429219	HCF	heart:	n/a
22	chr2:133429169-133429219	AG09309	skin:	n/a
23	chr2:133429169-133429219	ovcar-3	ovarian:	n/a
24	chr2:133429169-133429219	SK-N-SH_RA	brain:	n/a
25	chr2:133429169-133429219	PrEC	prostate:	n/a
26	chr2:133429169-133429219	A549	lung:	n/a
27	chr2:133429169-133429219	AG09319	gingival:	n/a
28	chr2:133429169-133429219	K562	blood:	n/a
29	chr2:133429169-133429219	RPTEC	kidney:	n/a
30	chr2:133429169-133429219	Caco-2	colon:	n/a
31	chr2:133429169-133429219	HCT-116	colon:	n/a
32	chr2:133429169-133429219	HepG2	liver:	n/a
33	chr2:133429169-133429219	BJ	skin:	n/a
34	chr2:133429169-133429219	HMEC	breast:	n/a
35	chr2:133429169-133429219	SKMC	muscle:	n/a
36	chr2:133429169-133429219	Jurkat	blood:	n/a
37	chr2:133429169-133429219	BE2_C	brain:	n/a
38	chr2:133429169-133429219	GM06990	blood:	n/a
39	chr2:133429169-133429219	HRCEpiC	kidney:	n/a
40	chr2:133429169-133429219	IMR90	lung:	fetal
41	chr2:133429169-133429219	U87	brain:	n/a
42	chr2:133429169-133429219	NH-A	brain:	n/a
43	chr2:133429169-133429219	NHDF-neo	bronchial:	n/a
44	chr2:133429169-133429219	T-47D	breast:	n/a
45	chr2:133429169-133429219	HNPCEpiC	eye:	n/a
46	chr2:133429169-133429219	HAEpiC	amniotic membrane:	n/a
47	chr2:133429169-133429219	HRPEpiC	eye:	n/a
48	chr2:133429169-133429219	GM12891	blood:	n/a
49	chr2:133429169-133429219	ECC-1	luminal epithelium:	n/a
50	chr2:133429169-133429219	AG04450	lung:	fetal

Variant related genes	Relation type
LYPD1	TF binding region
LYPD1	CpG island

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs12622583	0.87[AFR][1000 genomes]
rs16840026	0.87[AFR][1000 genomes]
rs57889347	0.87[AFR][1000 genomes]
rs58905085	0.87[AFR][1000 genomes]
rs60306901	0.87[AFR][1000 genomes]
rs73955785	0.87[AFR][1000 genomes]
rs73955786	0.87[AFR][1000 genomes]
rs73957610	0.87[AFR][1000 genomes]
rs73957613	0.87[AFR][1000 genomes]
rs73957614	0.87[AFR][1000 genomes]
rs73957617	0.87[AFR][1000 genomes]
rs73957624	0.87[AFR][1000 genomes]
rs73957626	0.87[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011421	chr2:132895241-133682185	Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv875137	chr2:133167263-133714142	Enhancers Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv583158	chr2:133316092-133862100	Weak transcription ZNF genes & repeats Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	nsv875138	chr2:133410921-133761794	Enhancers Bivalent/Poised TSS Strong transcription Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
5	esv3393724	chr2:133427132-133429630	Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:133425400-133429200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
2	chr2:133425800-133429200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
3	chr2:133425800-133429200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
4	chr2:133425800-133429200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr2:133425800-133429200	Active TSS	Fetal Kidney	kidney
6	chr2:133426000-133429200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
7	chr2:133426000-133429400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
8	chr2:133426000-133429400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
9	chr2:133426600-133429200	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr2:133428000-133429200	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr2:133428000-133429200	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
12	chr2:133428000-133429400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr2:133428000-133429400	Flanking Active TSS	HUVEC	blood vessel
14	chr2:133428200-133429200	Flanking Active TSS	Osteobl	bone
15	chr2:133428200-133429400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr2:133428400-133429200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr2:133428400-133429200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr2:133428400-133429400	Bivalent Enhancer	Stomach Mucosa	stomach
19	chr2:133428400-133429400	Enhancers	HMEC	breast
20	chr2:133428600-133429200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr2:133428600-133429200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr2:133428600-133429200	Flanking Active TSS	Hela-S3	cervix
23	chr2:133428600-133429400	Enhancers	HSMMtube	muscle
24	chr2:133428800-133429200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr2:133428800-133429200	Active TSS	Fetal Brain Female	brain
26	chr2:133428800-133429400	Active TSS	ES-I3 Cell Line	embryonic stem cell
27	chr2:133428800-133429400	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
28	chr2:133428800-133429400	Active TSS	H9 Cell Line	embryonic stem cell
29	chr2:133428800-133429400	Enhancers	NHLF	lung
30	chr2:133428800-133430000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr2:133428800-133431600	Weak transcription	Psoas Muscle	Psoas
32	chr2:133429000-133429200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
33	chr2:133429000-133429200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr2:133429000-133429200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
35	chr2:133429000-133429200	Enhancers	Cortex derived primary cultured neurospheres	brain
36	chr2:133429000-133429200	Enhancers	Brain Anterior Caudate	brain
37	chr2:133429000-133429200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
38	chr2:133429000-133429200	Enhancers	Fetal Brain Male	brain
39	chr2:133429000-133429400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr2:133429000-133429400	Bivalent Enhancer	Fetal Heart	heart
41	chr2:133429000-133429400	Active TSS	A549	lung
42	chr2:133429000-133429400	Enhancers	HSMM	muscle
43	chr2:133429000-133429400	Active TSS	NH-A	brain
44	chr2:133429000-133429600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr2:133429000-133429600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr2:133429000-133429600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr2:133429000-133429600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr2:133429000-133429600	Enhancers	NHEK	skin

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