Variant report

Variant	rs1980192
Chromosome Location	chr3:141456826-141456827
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	USF1	chr3:141456809-141457216	ECC-1	luminal epithelium:	n/a	chr3:141457009-141457020
2	RCOR1	chr3:141456746-141457497	GM12878	blood:	n/a	n/a
3	POLR2A	chr3:141456722-141457488	HepG2	liver:	n/a	n/a
4	YY1	chr3:141456743-141458210	A549	lung:	n/a	chr3:141457539-141457553 chr3:141456973-141456987 chr3:141457545-141457554 chr3:141458092-141458108 chr3:141457556-141457567 chr3:141457540-141457554
5	ARID3A	chr3:141456675-141457295	K562	blood:	n/a	n/a
6	HDAC2	chr3:141456751-141457111	K562	blood:	n/a	n/a
7	SIN3AK20	chr3:141456560-141458361	MCF-7	breast:	n/a	n/a
8	HDAC2	chr3:141456706-141457471	MCF-7	breast:	n/a	n/a
9	RUNX3	chr3:141456680-141458014	GM12878	blood:	n/a	n/a
10	JUND	chr3:141456524-141457709	GM12878	blood:	n/a	chr3:141456990-141456999 chr3:141457015-141457024
11	POLR2A	chr3:141456756-141457711	H1-hESC	embryonic stem cell:	n/a	n/a
12	RAD21	chr3:141456427-141458407	SK-N-SH	brain:	n/a	chr3:141456992-141457002 chr3:141457004-141457017 chr3:141457531-141457544
13	MYC	chr3:141456687-141458339	K562	blood:	n/a	chr3:141456976-141456986
14	SMC3	chr3:141456677-141457924	Hela-S3	cervix:	n/a	chr3:141457547-141457557
15	POU2F2	chr3:141456729-141457136	GM12878	blood:	n/a	n/a
16	POLR2A	chr3:141456637-141458013	GM12892	blood:	n/a	n/a
17	POLR2A	chr3:141456749-141457604	A549	lung:	n/a	n/a
18	RAD21	chr3:141456648-141457937	HCT-116	colon:	n/a	chr3:141456992-141457002 chr3:141457004-141457017 chr3:141457531-141457544
19	SP1	chr3:141456495-141457582	HCT-116	colon:	n/a	chr3:141456975-141456986 chr3:141456987-141456998 chr3:141456975-141456987 chr3:141456976-141456985 chr3:141456975-141456987 chr3:141456977-141456986 chr3:141456976-141456986 chr3:141456989-141456998
20	MAFK	chr3:141456805-141457122	HepG2	liver:	n/a	n/a
21	USF1	chr3:141456770-141457182	A549	lung:	n/a	chr3:141457009-141457020
22	BATF	chr3:141456813-141457348	GM12878	blood:	n/a	chr3:141457013-141457026
23	POLR2A	chr3:141456606-141457626	U87	brain:	n/a	n/a
24	TAF1	chr3:141456691-141457329	SK-N-SH	brain:	n/a	n/a
25	ATF3	chr3:141456760-141457281	H1-hESC	embryonic stem cell:	n/a	chr3:141457016-141457023 chr3:141457004-141457015 chr3:141457015-141457026 chr3:141457013-141457026 chr3:141457014-141457027 chr3:141457016-141457026 chr3:141457015-141457035 chr3:141457010-141457019 chr3:141457014-141457025 chr3:141457015-141457023 chr3:141457016-141457024 chr3:141457013-141457023 chr3:141457012-141457025 chr3:141456989-141456998 chr3:141457013-141457026 chr3:141457012-141457027 chr3:141457004-141457024
26	NRF1	chr3:141456493-141457521	SK-N-SH	brain:	n/a	chr3:141456879-141456890 chr3:141456880-141456894 chr3:141456877-141456891
27	RCOR1	chr3:141456628-141458176	Hela-S3	cervix:	n/a	n/a
28	NFYB	chr3:141456812-141457408	K562	blood:	n/a	chr3:141457030-141457045 chr3:141457033-141457048
29	TAF1	chr3:141456670-141457743	MCF-7	breast:	n/a	n/a
30	USF1	chr3:141456816-141457177	SK-N-SH_RA	brain:	n/a	chr3:141457009-141457020
31	RUNX3	chr3:141456578-141458042	GM12878	blood:	n/a	n/a
32	HMGN3	chr3:141456791-141458104	K562	blood:	n/a	n/a
33	FOXM1	chr3:141456593-141457546	GM12878	blood:	n/a	n/a
34	ATF3	chr3:141456803-141457236	H1-hESC	embryonic stem cell:	n/a	chr3:141457016-141457023 chr3:141457004-141457015 chr3:141457015-141457026 chr3:141457013-141457026 chr3:141457014-141457027 chr3:141457016-141457026 chr3:141457015-141457035 chr3:141457010-141457019 chr3:141457014-141457025 chr3:141457015-141457023 chr3:141457016-141457024 chr3:141457013-141457023 chr3:141457012-141457025 chr3:141456989-141456998 chr3:141457013-141457026 chr3:141457012-141457027 chr3:141457004-141457024
35	MYBL2	chr3:141456506-141457459	HepG2	liver:	n/a	n/a
36	E2F4	chr3:141456767-141457512	K562	blood:	n/a	chr3:141456989-141456998 chr3:141457491-141457501 chr3:141456980-141456990 chr3:141457016-141457025 chr3:141457014-141457023 chr3:141457035-141457044
37	E2F4	chr3:141456783-141457304	MCF10A-Er-Src	breast:	n/a	chr3:141456989-141456998 chr3:141456980-141456990 chr3:141457016-141457025 chr3:141457014-141457023 chr3:141457035-141457044
38	MXI1	chr3:141456771-141458210	Hela-S3	cervix:	n/a	n/a
39	GATA2	chr3:141456692-141457001	HUVEC	blood vessel:	n/a	n/a
40	TCF7L2	chr3:141456768-141457580	HCT-116	colon:	n/a	n/a
41	TAF1	chr3:141456718-141457928	SK-N-SH	brain:	n/a	n/a
42	POLR2A	chr3:141456702-141457432	K562	blood:	n/a	n/a
43	POLR2A	chr3:141456573-141457631	SK-N-MC	brain:	n/a	n/a
44	POLR2A	chr3:141456729-141457831	K562	blood:	n/a	n/a
45	SMC3	chr3:141456815-141457427	K562	blood:	n/a	n/a
46	POLR2A	chr3:141456669-141458042	GM18526	blood:	n/a	n/a
47	SP1	chr3:141456706-141457236	HepG2	liver:	n/a	chr3:141456975-141456986 chr3:141456987-141456998 chr3:141456975-141456987 chr3:141456976-141456985 chr3:141456975-141456987 chr3:141456977-141456986 chr3:141456976-141456986 chr3:141456989-141456998
48	SRF	chr3:141456760-141457240	H1-hESC	embryonic stem cell:	n/a	chr3:141456976-141456986 chr3:141456989-141456999
49	POLR2A	chr3:141456617-141458146	MCF-7	breast:	n/a	n/a
50	PAX5	chr3:141456803-141457587	GM12892	blood:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:141456799-141456849	BE2_C	brain:	n/a
2	chr3:141456799-141456849	HCT-116	colon:	n/a
3	chr3:141456799-141456849	MCF10A-Er-Src	breast:	n/a
4	chr3:141456799-141456849	GM12892	blood:	n/a
5	chr3:141456799-141456849	U87	brain:	n/a
6	chr3:141456799-141456849	NHBE	bronchial:	n/a
7	chr3:141456799-141456849	MCF-7	breast:	n/a
8	chr3:141456799-141456849	LNCaP	prostate:	n/a
9	chr3:141456799-141456849	GM19239	blood:	n/a
10	chr3:141456799-141456849	GM06990	blood:	n/a
11	chr3:141456799-141456849	AG10803	skin:	n/a
12	chr3:141456799-141456849	HPAEpiC	pulmonary alveolar:	n/a
13	chr3:141456799-141456849	HEK293	kidney:	embryo
14	chr3:141456799-141456849	RPTEC	kidney:	n/a
15	chr3:141456799-141456849	CMK	blood:	n/a
16	chr3:141456799-141456849	IMR90	lung:	fetal
17	chr3:141456799-141456849	AG09319	gingival:	n/a
18	chr3:141456799-141456849	HepG2	liver:	n/a
19	chr3:141456799-141456849	HMEC	breast:	n/a
20	chr3:141456799-141456849	PrEC	prostate:	n/a
21	chr3:141456799-141456849	HUVEC	blood vessel:	n/a
22	chr3:141456799-141456849	HRCEpiC	kidney:	n/a
23	chr3:141456799-141456849	HRE	kidney:	n/a
24	chr3:141456799-141456849	HEEpiC	esophagus:	n/a
25	chr3:141456799-141456849	ovcar-3	ovarian:	n/a
26	chr3:141456799-141456849	Jurkat	blood:	n/a
27	chr3:141456799-141456849	H1-hESC	embryonic stem cell:	embryo
28	chr3:141456799-141456849	AG04450	lung:	fetal
29	chr3:141456799-141456849	GM12878	blood:	n/a
30	chr3:141456799-141456849	SK-N-SH_RA	brain:	n/a
31	chr3:141456799-141456849	BJ	skin:	n/a
32	chr3:141456799-141456849	Hela-S3	cervix:	n/a
33	chr3:141456799-141456849	A549	lung:	n/a
34	chr3:141456799-141456849	NT2-D1	testis:	n/a
35	chr3:141456799-141456849	SK-N-SH	brain:	n/a
36	chr3:141456799-141456849	NB4	blood:	n/a
37	chr3:141456799-141456849	SK-N-MC	brain:	n/a
38	chr3:141456799-141456849	AG04449	skin:	fetal
39	chr3:141456799-141456849	HL-60	blood:	n/a
40	chr3:141456799-141456849	HCF	heart:	n/a
41	chr3:141456799-141456849	PFSK-1	brain:	n/a
42	chr3:141456799-141456849	SAEC	small airway:	n/a
43	chr3:141456799-141456849	HCM	heart:	n/a
44	chr3:141456799-141456849	GM12891	blood:	n/a
45	chr3:141456799-141456849	HAEpiC	amniotic membrane:	n/a
46	chr3:141456799-141456849	AG09309	skin:	n/a
47	chr3:141456799-141456849	T-47D	breast:	n/a
48	chr3:141456799-141456849	ProgFib	skin:	n/a
49	chr3:141456799-141456849	NHDF-neo	bronchial:	n/a
50	chr3:141456799-141456849	HNPCEpiC	eye:	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:141455674..141460093-chr3:141592801..141597430,19	MCF-7	breast:
2	chr3:141452499..141459593-chr3:141591792..141599045,17	MCF-7	breast:
3	chr3:141357032..141359290-chr3:141454667..141456901,2	K562	blood:
4	chr3:141456656..141457567-chr3:141593967..141595178,5	K562	blood:
5	chr3:141456676..141459122-chr3:141866884..141869547,2	MCF-7	breast:
6	chr3:141455466..141460652-chr3:141593125..141598625,15	K562	blood:
7	chr15:75248806..75249569-chr3:141456730..141457559,2	Hela-S3	cervix:
8	chr3:141456347..141457648-chr3:141594019..141595007,11	MCF-7	breast:
9	chr3:141455463..141459614-chr3:141593520..141599146,20	K562	blood:
10	chr3:141455584..141459326-chr3:141464266..141467931,6	MCF-7	breast:
11	chr3:141456324..141457198-chr3:141594736..141595366,2	Hela-S3	cervix:

Variant related genes	Relation type
RNF7	TF binding region
RNF7	CpG island
ENSG00000178718	Chromatin interaction
ENSG00000114125	Chromatin interaction
ENSG00000198794	Chromatin interaction
ENSG00000114126	Chromatin interaction
ENSG00000069849	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1105082	0.86[ASN][1000 genomes]
rs11542226	0.85[EUR][1000 genomes]
rs1533501	0.80[EUR][1000 genomes]
rs16851704	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16851717	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16851740	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16851752	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1879284	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1879285	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1980191	0.98[ASN][1000 genomes]
rs3773840	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4538350	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4588340	0.80[EUR][1000 genomes]
rs57394236	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs57805567	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs57983026	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58115387	0.85[EUR][1000 genomes]
rs58300294	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs59998648	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60806348	0.84[ASN][1000 genomes]
rs60938827	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61278509	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs61294533	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs61632965	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6783647	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6783736	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73872318	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73872319	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73872322	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73872326	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7632069	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7642922	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7643689	0.85[EUR][1000 genomes]
rs9789959	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9789973	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949709	chr3:141295050-142178144	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv877552	chr3:141420562-141466147	Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1980192	RNF7	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:141455000-141457000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr3:141456000-141457000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
3	chr3:141456200-141457800	Active TSS	Primary T cells from cord blood	blood
4	chr3:141456400-141457000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
5	chr3:141456400-141457200	Active TSS	HepG2	liver
6	chr3:141456400-141458200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr3:141456600-141457000	Flanking Active TSS	Primary B cells from cord blood	blood
8	chr3:141456600-141457000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
9	chr3:141456600-141457200	Active TSS	Primary T helper naive cells fromperipheralblood	blood
10	chr3:141456600-141457200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr3:141456600-141457200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr3:141456600-141457200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr3:141456600-141457600	Active TSS	Skeletal Muscle Female	skeletal muscle
14	chr3:141456600-141457800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr3:141456600-141457800	Active TSS	Adipose Nuclei	Adipose
16	chr3:141456600-141457800	Active TSS	Liver	Liver
17	chr3:141456600-141458000	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
18	chr3:141456600-141458000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr3:141456600-141458000	Active TSS	Fetal Heart	heart
20	chr3:141456600-141458200	Active TSS	Primary T helper naive cells from peripheral blood	blood
21	chr3:141456600-141458200	Active TSS	Primary T helper cells PMA-I stimulated	--
22	chr3:141456600-141458200	Active TSS	Primary T killer naive cells fromperipheralblood	blood
23	chr3:141456600-141458200	Active TSS	Brain Cingulate Gyrus	brain
24	chr3:141456600-141458200	Active TSS	Colon Smooth Muscle	Colon
25	chr3:141456600-141458200	Active TSS	Left Ventricle	heart
26	chr3:141456600-141458200	Active TSS	Placenta Amnion	Placenta Amnion
27	chr3:141456600-141458200	Active TSS	Skeletal Muscle Male	skeletal muscle
28	chr3:141456600-141458200	Active TSS	Stomach Mucosa	stomach
29	chr3:141456600-141458200	Active TSS	Hela-S3	cervix
30	chr3:141456600-141458200	Active TSS	Osteobl	bone
31	chr3:141456600-141458400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
32	chr3:141456600-141458400	Active TSS	H1 Cell Line	embryonic stem cell
33	chr3:141456600-141458400	Active TSS	H9 Cell Line	embryonic stem cell
34	chr3:141456600-141458400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr3:141456600-141458400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr3:141456600-141458400	Active TSS	HUES48 Cell Line	embryonic stem cell
37	chr3:141456600-141458400	Active TSS	iPS-15b Cell Line	embryonic stem cell
38	chr3:141456600-141458400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr3:141456600-141458400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr3:141456600-141458400	Active TSS	Primary T killer memory cells from peripheral blood	blood
41	chr3:141456600-141458400	Active TSS	Cortex derived primary cultured neurospheres	brain
42	chr3:141456600-141458400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr3:141456600-141458400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr3:141456600-141458400	Active TSS	Brain Anterior Caudate	brain
45	chr3:141456600-141458400	Active TSS	Brain Inferior Temporal Lobe	brain
46	chr3:141456600-141458400	Active TSS	Brain Substantia Nigra	brain
47	chr3:141456600-141458400	Active TSS	Duodenum Mucosa	Duodenum
48	chr3:141456600-141458400	Active TSS	Duodenum Smooth Muscle	Duodenum
49	chr3:141456600-141458400	Active TSS	Fetal Lung	lung
50	chr3:141456600-141458400	Active TSS	Fetal Stomach	stomach

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