Variant report

Variant	rs6834665
Chromosome Location	chr4:82393305-82393306
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	EBF1	chr4:82392973-82393750	GM12878	blood:	n/a	n/a
2	FOXA1	chr4:82393148-82393461	ECC-1	luminal epithelium:	n/a	n/a
3	FOXP2	chr4:82392812-82393663	SK-N-MC	brain:	n/a	n/a
4	RAD21	chr4:82392520-82393781	H1-hESC	embryonic stem cell:	n/a	chr4:82393259-82393272
5	PML	chr4:82393120-82393547	GM12878	blood:	n/a	chr4:82393496-82393504
6	FOXP2	chr4:82393218-82393448	SK-N-MC	brain:	n/a	n/a
7	EGR1	chr4:82392904-82393416	H1-hESC	embryonic stem cell:	n/a	chr4:82393250-82393260 chr4:82393170-82393177 chr4:82393170-82393183 chr4:82393169-82393183 chr4:82393171-82393182 chr4:82393171-82393180 chr4:82393171-82393181 chr4:82393170-82393183 chr4:82393171-82393182 chr4:82393171-82393181 chr4:82393170-82393183 chr4:82393169-82393184 chr4:82393167-82393181
8	MAX	chr4:82392396-82393816	ECC-1	luminal epithelium:	n/a	chr4:82393763-82393772 chr4:82393172-82393181 chr4:82392754-82392764
9	EGR1	chr4:82392882-82393563	HCT-116	colon:	n/a	chr4:82393250-82393260 chr4:82393170-82393177 chr4:82393170-82393183 chr4:82393169-82393183 chr4:82393171-82393182 chr4:82393171-82393180 chr4:82393171-82393181 chr4:82393170-82393183 chr4:82393171-82393182 chr4:82393171-82393181 chr4:82393170-82393183 chr4:82393169-82393184 chr4:82393167-82393181
10	POLR2A	chr4:82393249-82393326	A549	lung:	n/a	n/a
11	POLR2A	chr4:82392771-82393537	HL-60	blood:	n/a	n/a
12	RELA	chr4:82392986-82393739	GM19099	blood:	n/a	n/a
13	RFX5	chr4:82393033-82393334	GM12878	blood:	n/a	n/a
14	E2F6	chr4:82392341-82393315	H1-hESC	embryonic stem cell:	n/a	chr4:82392750-82392762
15	POLR2A	chr4:82392920-82393361	MCF-7	breast:	n/a	n/a
16	JUND	chr4:82393068-82393403	K562	blood:	n/a	n/a
17	NFYB	chr4:82392981-82393335	GM12878	blood:	n/a	n/a
18	POLR2A	chr4:82392766-82393451	MCF-7	breast:	n/a	n/a
19	CEBPB	chr4:82393192-82393713	IMR90	lung:	n/a	n/a
20	POLR2A	chr4:82392797-82393440	MCF-7	breast:	n/a	n/a
21	PAX5	chr4:82392974-82393621	GM12878	blood:	n/a	chr4:82393328-82393347
22	EGR1	chr4:82392817-82393674	ECC-1	luminal epithelium:	n/a	chr4:82393250-82393260 chr4:82393170-82393177 chr4:82393170-82393183 chr4:82393169-82393183 chr4:82393171-82393182 chr4:82393171-82393180 chr4:82393171-82393181 chr4:82393170-82393183 chr4:82393171-82393182 chr4:82393171-82393181 chr4:82393170-82393183 chr4:82393169-82393184 chr4:82393167-82393181
23	BCLAF1	chr4:82393160-82393775	GM12878	blood:	n/a	chr4:82393178-82393191
24	MAX	chr4:82392993-82393457	HepG2	liver:	n/a	chr4:82393172-82393181
25	HA-E2F1	chr4:82391721-82393739	MCF-7	breast:	n/a	chr4:82392052-82392066 chr4:82392054-82392061 chr4:82392750-82392762
26	MXI1	chr4:82392906-82393761	GM12878	blood:	n/a	n/a
27	MAX	chr4:82392307-82393947	ECC-1	luminal epithelium:	n/a	chr4:82393763-82393772 chr4:82393172-82393181 chr4:82392754-82392764
28	RUNX3	chr4:82393015-82393679	GM12878	blood:	n/a	n/a
29	POLR2A	chr4:82393103-82393367	GM12878	blood:	n/a	n/a
30	SP1	chr4:82392902-82393414	GM12878	blood:	n/a	n/a
31	CTCF	chr4:82393302-82393306	Spleen_OC	spleen:	n/a	n/a
32	PAX5	chr4:82393018-82393326	GM12892	blood:	n/a	n/a
33	POU2F2	chr4:82393136-82393717	GM12878	blood:	n/a	chr4:82393433-82393455 chr4:82393439-82393450
34	EP300	chr4:82393001-82393600	GM12878	blood:	n/a	n/a
35	CTBP2	chr4:82392028-82393566	H1-hESC	embryonic stem cell:	n/a	n/a
36	EGR1	chr4:82392936-82393400	K562	blood:	n/a	chr4:82393250-82393260 chr4:82393170-82393177 chr4:82393170-82393183 chr4:82393169-82393183 chr4:82393171-82393182 chr4:82393171-82393180 chr4:82393171-82393181 chr4:82393170-82393183 chr4:82393171-82393182 chr4:82393171-82393181 chr4:82393170-82393183 chr4:82393169-82393184 chr4:82393167-82393181
37	TAL1	chr4:82393170-82393386	K562	blood:	n/a	n/a
38	MAX	chr4:82392991-82393370	K562	blood:	n/a	chr4:82393172-82393181
39	EBF1	chr4:82392779-82393673	GM12878	blood:	n/a	chr4:82392827-82392836
40	ESR1	chr4:82392979-82393505	ECC-1	luminal epithelium:	n/a	n/a
41	EGR1	chr4:82393043-82393339	GM12878	blood:	n/a	chr4:82393250-82393260 chr4:82393170-82393177 chr4:82393170-82393183 chr4:82393169-82393183 chr4:82393171-82393182 chr4:82393171-82393180 chr4:82393171-82393181 chr4:82393170-82393183 chr4:82393171-82393182 chr4:82393171-82393181 chr4:82393170-82393183 chr4:82393169-82393184 chr4:82393167-82393181
42	EGR1	chr4:82392916-82393533	MCF-7	breast:	n/a	chr4:82393250-82393260 chr4:82393170-82393177 chr4:82393170-82393183 chr4:82393169-82393183 chr4:82393171-82393182 chr4:82393171-82393180 chr4:82393171-82393181 chr4:82393170-82393183 chr4:82393171-82393182 chr4:82393171-82393181 chr4:82393170-82393183 chr4:82393169-82393184 chr4:82393167-82393181
43	EGR1	chr4:82392839-82393542	ECC-1	luminal epithelium:	n/a	chr4:82393250-82393260 chr4:82393170-82393177 chr4:82393170-82393183 chr4:82393169-82393183 chr4:82393171-82393182 chr4:82393171-82393180 chr4:82393171-82393181 chr4:82393170-82393183 chr4:82393171-82393182 chr4:82393171-82393181 chr4:82393170-82393183 chr4:82393169-82393184 chr4:82393167-82393181
44	ZNF263	chr4:82391497-82393768	HEK293-T-REx	kidney:	n/a	n/a
45	MAX	chr4:82392924-82393542	GM12878	blood:	n/a	chr4:82393172-82393181
46	SMC3	chr4:82393185-82393669	GM12878	blood:	n/a	n/a
47	POLR2A	chr4:82392673-82393886	PBDE	blood:	n/a	n/a
48	POLR2A	chr4:82392904-82393416	K562	blood:	n/a	n/a
49	EP300	chr4:82393078-82393383	GM12878	blood:	n/a	n/a
50	RCOR1	chr4:82392861-82393755	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:82392247..82394728-chr4:83351803..83353310,2	MCF-7	breast:

Variant related genes	Relation type
RASGEF1B	TF binding region
ENSG00000145293	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10010140	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10010394	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10012642	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10015146	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10023826	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12500201	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12502814	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13102560	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13111699	1.00[ASN][1000 genomes]
rs13128387	0.90[ASN][1000 genomes]
rs13131664	0.95[ASN][1000 genomes]
rs16998600	0.97[ASN][1000 genomes]
rs17005142	1.00[ASN][1000 genomes]
rs17005144	1.00[ASN][1000 genomes]
rs17005145	1.00[ASN][1000 genomes]
rs28479652	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28767523	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28827174	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34128580	1.00[ASN][1000 genomes]
rs34749111	0.90[ASN][1000 genomes]
rs35010226	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35149381	0.95[ASN][1000 genomes]
rs35991185	1.00[ASN][1000 genomes]
rs36026752	1.00[ASN][1000 genomes]
rs41523946	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4693274	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4693275	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4693276	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4693277	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62303604	1.00[ASN][1000 genomes]
rs6535252	0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6819741	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6819989	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6825177	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7660392	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7678464	0.90[ASN][1000 genomes]
rs7683852	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7684580	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7688827	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7690069	0.95[ASN][1000 genomes]
rs7691170	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9307784	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999729	chr4:81802554-82627820	Genic enhancers Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv537156	chr4:81802554-82627820	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv829986	chr4:82345163-82509860	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:82389800-82393800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr4:82390400-82393600	Active TSS	Lung	lung
3	chr4:82390600-82393400	Active TSS	Liver	Liver
4	chr4:82390600-82393400	Active TSS	Duodenum Mucosa	Duodenum
5	chr4:82390600-82393600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr4:82390600-82393600	Active TSS	Esophagus	oesophagus
7	chr4:82390600-82394200	Active TSS	Duodenum Smooth Muscle	Duodenum
8	chr4:82391000-82393600	Active TSS	Aorta	Aorta
9	chr4:82391000-82393600	Active TSS	Brain Inferior Temporal Lobe	brain
10	chr4:82391000-82393600	Active TSS	Stomach Mucosa	stomach
11	chr4:82391000-82393800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
12	chr4:82391000-82393800	Active TSS	Colonic Mucosa	Colon
13	chr4:82391000-82393800	Active TSS	Right Ventricle	heart
14	chr4:82391200-82393400	Active TSS	Brain Substantia Nigra	brain
15	chr4:82391200-82393400	Active TSS	Placenta	Placenta
16	chr4:82391200-82393600	Active TSS	Brain Angular Gyrus	brain
17	chr4:82391200-82393600	Active TSS	Brain Hippocampus Middle	brain
18	chr4:82391200-82393600	Active TSS	Pancreatic Islets	Pancreatic Islet
19	chr4:82391200-82393800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
20	chr4:82391400-82393400	Active TSS	Primary T killer memory cells from peripheral blood	blood
21	chr4:82391400-82393400	Active TSS	Brain Cingulate Gyrus	brain
22	chr4:82391400-82393400	Active TSS	Spleen	Spleen
23	chr4:82391400-82393600	Active TSS	Left Ventricle	heart
24	chr4:82391400-82393600	Active TSS	Ovary	ovary
25	chr4:82391400-82393600	Active TSS	Monocytes-CD14+_RO01746	blood
26	chr4:82391400-82393800	Active TSS	Psoas Muscle	Psoas
27	chr4:82391400-82394000	Active TSS	Fetal Intestine Large	intestine
28	chr4:82391600-82393400	Active TSS	Primary B cells from cord blood	blood
29	chr4:82391600-82393400	Active TSS	Primary T helper cells PMA-I stimulated	--
30	chr4:82391600-82393400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr4:82391600-82393400	Active TSS	Fetal Brain Male	brain
32	chr4:82391600-82393400	Active TSS	Fetal Kidney	kidney
33	chr4:82391600-82393400	Active TSS	Small Intestine	intestine
34	chr4:82391600-82393600	Active TSS	Gastric	stomach
35	chr4:82391600-82393600	Active TSS	Sigmoid Colon	Sigmoid Colon
36	chr4:82391800-82393400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr4:82391800-82393600	Active TSS	Primary B cells from peripheral blood	blood
38	chr4:82391800-82393600	Active TSS	Primary T cells from cord blood	blood
39	chr4:82391800-82393600	Active TSS	Primary T helper naive cells from peripheral blood	blood
40	chr4:82391800-82393600	Active TSS	Brain Anterior Caudate	brain
41	chr4:82391800-82393600	Active TSS	Brain Germinal Matrix	brain
42	chr4:82391800-82393600	Active TSS	Fetal Brain Female	brain
43	chr4:82391800-82393600	Active TSS	Thymus	Thymus
44	chr4:82391800-82393600	Bivalent/Poised TSS	HSMMtube	muscle
45	chr4:82391800-82394000	Active TSS	Right Atrium	heart
46	chr4:82392000-82393400	Active TSS	Breast Myoepithelial Primary Cells	Breast
47	chr4:82392000-82393400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
48	chr4:82392000-82393400	Active TSS	Fetal Lung	lung
49	chr4:82392000-82393400	Active TSS	Rectal Mucosa Donor 29	rectum
50	chr4:82392000-82393600	Active TSS	ES-WA7 Cell Line	embryonic stem cell

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