Variant report

Variant	rs3806285
Chromosome Location	chr1:228870664-228870665
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	MAZ	chr1:228870509-228872073	IMR90	lung:	n/a	chr1:228870867-228870876
2	RAD21	chr1:228870648-228871417	HepG2	liver:	n/a	chr1:228870817-228870830
3	RAD21	chr1:228870658-228871320	SK-N-SH_RA	brain:	n/a	chr1:228870817-228870830
4	HA-E2F1	chr1:228870624-228871464	MCF-7	breast:	n/a	chr1:228871285-228871295 chr1:228870871-228870886
5	ZNF263	chr1:228870655-228871471	HEK293-T-REx	kidney:	n/a	chr1:228871402-228871411 chr1:228870931-228870940
6	MYC	chr1:228870476-228870743	MCF10A-Er-Src	breast:	n/a	n/a
7	CTCF	chr1:228870560-228870710	BE2_C	brain:	n/a	n/a
8	HDAC2	chr1:228870635-228871566	MCF-7	breast:	n/a	chr1:228870867-228870876 chr1:228871475-228871484
9	CTCF	chr1:228870401-228871752	A549	lung:	n/a	chr1:228870813-228870831 chr1:228870816-228870829
10	RAD21	chr1:228870578-228871368	A549	lung:	n/a	chr1:228870817-228870830
11	RAD21	chr1:228870386-228872827	SK-N-SH	brain:	n/a	chr1:228870817-228870830
12	SMC3	chr1:228870446-228872446	SK-N-SH	brain:	n/a	n/a
13	RAD21	chr1:228870520-228871553	A549	lung:	n/a	chr1:228870817-228870830
14	RAD21	chr1:228870641-228871621	SK-N-SH_RA	brain:	n/a	chr1:228870817-228870830
15	CTCF	chr1:228870640-228870790	HVMF	connective:	n/a	n/a
16	SPI1	chr1:228870632-228871132	HL-60	blood:	n/a	chr1:228870879-228870892
17	TCF12	chr1:228870590-228871520	A549	lung:	n/a	n/a
18	MXI1	chr1:228870038-228872688	SK-N-SH	brain:	n/a	n/a
19	CTCF	chr1:228870560-228870710	GM12868	blood:	n/a	n/a
20	RAD21	chr1:228870642-228871410	Hela-S3	cervix:	n/a	chr1:228870817-228870830
21	RAD21	chr1:228870658-228871462	HepG2	liver:	n/a	chr1:228870817-228870830
22	CTCF	chr1:228870640-228870790	GM12872	blood:	n/a	n/a
23	RAD21	chr1:228870540-228871576	HCT-116	colon:	n/a	chr1:228870817-228870830
24	SMC3	chr1:228870593-228871587	Hela-S3	cervix:	n/a	n/a
25	CTCF	chr1:228870640-228870790	WERI-Rb-1	eye:	n/a	n/a
26	CTCF	chr1:228870560-228870710	HVMF	connective:	n/a	n/a
27	REST	chr1:228870403-228872185	H1-neurons	neurons:	n/a	chr1:228870949-228870962
28	CTCF	chr1:228870362-228871645	SK-N-SH	brain:	n/a	chr1:228870813-228870831 chr1:228870816-228870829
29	SIN3AK20	chr1:228870631-228871597	MCF-7	breast:	n/a	n/a
30	MXI1	chr1:228870383-228872478	IMR90	lung:	n/a	n/a
31	E2F4	chr1:228870490-228871329	MCF10A-Er-Src	breast:	n/a	chr1:228871285-228871295 chr1:228870871-228870886
32	CTCF	chr1:228870617-228871501	IMR90	lung:	n/a	chr1:228870813-228870831 chr1:228870816-228870829
33	MYC	chr1:228870487-228870668	MCF10A-Er-Src	breast:	n/a	n/a
34	CTCF	chr1:228870660-228870810	HUVEC	blood vessel:	n/a	n/a
35	RAD21	chr1:228870569-228871400	MCF-7	breast:	n/a	chr1:228870817-228870830
36	MAX	chr1:228870628-228872111	A549	lung:	n/a	chr1:228870867-228870876
37	RAD21	chr1:228870595-228871655	H1-hESC	embryonic stem cell:	n/a	chr1:228870817-228870830
38	RAD21	chr1:228870631-228871462	IMR90	lung:	n/a	chr1:228870817-228870830

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:228870629-228870679	GM19239	blood:	n/a
2	chr1:228870637-228870687	HAEpiC	amniotic membrane:	n/a
3	chr1:228870637-228870687	BJ	skin:	n/a
4	chr1:228870629-228870679	HRCEpiC	kidney:	n/a
5	chr1:228870629-228870679	ovcar-3	ovarian:	n/a
6	chr1:228870637-228870687	RPTEC	kidney:	n/a
7	chr1:228870629-228870679	HCPEpiC	choroid plexus:	n/a
8	chr1:228870637-228870687	ovcar-3	ovarian:	n/a
9	chr1:228870629-228870679	Jurkat	blood:	n/a
10	chr1:228870629-228870679	HAEpiC	amniotic membrane:	n/a
11	chr1:228870637-228870687	NH-A	brain:	n/a
12	chr1:228870629-228870679	HepG2	liver:	n/a
13	chr1:228870637-228870687	BE2_C	brain:	n/a
14	chr1:228870629-228870679	SAEC	small airway:	n/a
15	chr1:228870629-228870679	NH-A	brain:	n/a
16	chr1:228870637-228870687	Hepatocyte	liver:	n/a
17	chr1:228870637-228870687	U87	brain:	n/a
18	chr1:228870637-228870687	SKMC	muscle:	n/a
19	chr1:228870637-228870687	GM12891	blood:	n/a
20	chr1:228870629-228870679	HL-60	blood:	n/a
21	chr1:228870637-228870687	GM12878	blood:	n/a
22	chr1:228870637-228870687	AG09309	skin:	n/a
23	chr1:228870637-228870687	HMEC	breast:	n/a
24	chr1:228870629-228870679	HEEpiC	esophagus:	n/a
25	chr1:228870629-228870679	NT2-D1	testis:	n/a
26	chr1:228870629-228870679	HUVEC	blood vessel:	n/a
27	chr1:228870629-228870679	AG04450	lung:	fetal
28	chr1:228870637-228870687	AG04449	skin:	fetal
29	chr1:228870629-228870679	MCF-7	breast:	n/a
30	chr1:228870629-228870679	NHDF-neo	bronchial:	n/a
31	chr1:228870637-228870687	A549	lung:	n/a
32	chr1:228870629-228870679	PrEC	prostate:	n/a
33	chr1:228870629-228870679	NB4	blood:	n/a
34	chr1:228870637-228870687	AG10803	skin:	n/a
35	chr1:228870629-228870679	SK-N-MC	brain:	n/a
36	chr1:228870637-228870687	AG09319	gingival:	n/a
37	chr1:228870637-228870687	SAEC	small airway:	n/a
38	chr1:228870629-228870679	SKMC	muscle:	n/a
39	chr1:228870629-228870679	HMEC	breast:	n/a
40	chr1:228870629-228870679	NHBE	bronchial:	n/a
41	chr1:228870629-228870679	HCT-116	colon:	n/a
42	chr1:228870637-228870687	HRE	kidney:	n/a
43	chr1:228870629-228870679	LNCaP	prostate:	n/a
44	chr1:228870629-228870679	T-47D	breast:	n/a
45	chr1:228870629-228870679	ECC-1	luminal epithelium:	n/a
46	chr1:228870637-228870687	HPAEpiC	pulmonary alveolar:	n/a
47	chr1:228870629-228870679	AG09309	skin:	n/a
48	chr1:228870637-228870687	Jurkat	blood:	n/a
49	chr1:228870629-228870679	HEK293	kidney:	embryo
50	chr1:228870629-228870679	BJ	skin:	n/a

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

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1006797	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10489542	0.92[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1108502	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12059178	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12066510	0.80[CHB][hapmap]
rs12070785	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12075157	0.81[ASN][1000 genomes]
rs12076649	0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12077418	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12078927	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12092986	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12096381	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1535129	0.97[EUR][1000 genomes]
rs2009564	0.92[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs2180162	0.92[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2207704	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2295255	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34036301	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3820265	0.92[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4654625	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6667385	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6681268	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7532644	0.99[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7554565	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013051	chr1:228786702-228903706	Genic enhancers Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv997801	chr1:228786702-228975127	Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv870365	chr1:228788356-229267904	Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv998255	chr1:228791784-228919202	Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
5	nsv549299	chr1:228793246-229455876	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	nsv468316	chr1:228854703-228919202	Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
7	nsv549300	chr1:228854703-228919202	Active TSS Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
8	esv3405929	chr1:228869854-228872702	Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228868400-228870800	Weak transcription	Gastric	stomach
2	chr1:228869800-228871000	Enhancers	Fetal Brain Male	brain
3	chr1:228870200-228872000	Active TSS	Skeletal Muscle Male	skeletal muscle
4	chr1:228870200-228875400	Active TSS	Brain Angular Gyrus	brain
5	chr1:228870400-228870800	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr1:228870400-228870800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr1:228870400-228870800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr1:228870400-228870800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr1:228870400-228870800	Flanking Active TSS	Brain Germinal Matrix	brain
10	chr1:228870400-228870800	Flanking Active TSS	Fetal Brain Female	brain
11	chr1:228870400-228870800	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
12	chr1:228870400-228870800	Flanking Active TSS	Rectal Smooth Muscle	rectum
13	chr1:228870400-228870800	Flanking Active TSS	Stomach Smooth Muscle	stomach
14	chr1:228870400-228871000	Active TSS	Primary T killer memory cells from peripheral blood	blood
15	chr1:228870400-228871000	Flanking Bivalent TSS/Enh	Muscle Satellite Cultured Cells	--
16	chr1:228870400-228871000	Enhancers	Stomach Mucosa	stomach
17	chr1:228870400-228871000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
18	chr1:228870400-228872000	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
19	chr1:228870400-228872000	Active TSS	Fetal Stomach	stomach
20	chr1:228870400-228872200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
21	chr1:228870400-228872200	Active TSS	Rectal Mucosa Donor 29	rectum
22	chr1:228870400-228872400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
23	chr1:228870400-228872400	Bivalent/Poised TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr1:228870400-228872800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
25	chr1:228870400-228873200	Active TSS	Fetal Intestine Small	intestine
26	chr1:228870400-228873400	Active TSS	Fetal Intestine Large	intestine
27	chr1:228870400-228873800	Active TSS	Aorta	Aorta
28	chr1:228870400-228873800	Active TSS	Colonic Mucosa	Colon
29	chr1:228870400-228873800	Active TSS	Right Ventricle	heart
30	chr1:228870400-228874000	Active TSS	Brain Anterior Caudate	brain
31	chr1:228870400-228874200	Active TSS	Duodenum Smooth Muscle	Duodenum
32	chr1:228870600-228870800	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
33	chr1:228870600-228870800	Flanking Bivalent TSS/Enh	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr1:228870600-228870800	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
35	chr1:228870600-228870800	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
36	chr1:228870600-228870800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr1:228870600-228870800	Bivalent Enhancer	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr1:228870600-228870800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
39	chr1:228870600-228870800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
40	chr1:228870600-228870800	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr1:228870600-228870800	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr1:228870600-228870800	Flanking Active TSS	Brain Cingulate Gyrus	brain
43	chr1:228870600-228870800	Flanking Active TSS	Brain Hippocampus Middle	brain
44	chr1:228870600-228870800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
45	chr1:228870600-228870800	Flanking Bivalent TSS/Enh	Fetal Heart	heart
46	chr1:228870600-228870800	Flanking Active TSS	Fetal Muscle Trunk	muscle
47	chr1:228870600-228870800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
48	chr1:228870600-228870800	Bivalent Enhancer	Dnd41	blood
49	chr1:228870600-228870800	Flanking Active TSS	Hela-S3	cervix
50	chr1:228870600-228870800	Flanking Active TSS	HepG2	liver

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