Variant report

Variant	rs2802701
Chromosome Location	chr6:69344385-69344386
allele	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	EP300	chr6:69344018-69344602	K562	blood:	n/a	n/a
2	RAD21	chr6:69342384-69347457	SK-N-SH	brain:	n/a	chr6:69345907-69345917 chr6:69345020-69345034 chr6:69344689-69344699 chr6:69343839-69343849 chr6:69345328-69345338
3	RFX5	chr6:69342558-69347581	SK-N-SH	brain:	n/a	chr6:69344290-69344305 chr6:69346927-69346936 chr6:69344290-69344305
4	RAD21	chr6:69344336-69345415	SK-N-SH_RA	brain:	n/a	chr6:69345020-69345034 chr6:69344689-69344699 chr6:69345328-69345338
5	TAF1	chr6:69344279-69345456	H1-neurons	neurons:	n/a	n/a
6	POLR2A	chr6:69343624-69345670	H1-neurons	neurons:	n/a	n/a
7	TBL1XR1	chr6:69343992-69344519	K562	blood:	n/a	n/a
8	REST	chr6:69343340-69345936	H1-neurons	neurons:	n/a	n/a
9	SIN3A	chr6:69344357-69346221	H1-hESC	embryonic stem cell:	n/a	chr6:69345031-69345042
10	NRF1	chr6:69344071-69345747	SK-N-SH	brain:	n/a	chr6:69345080-69345091 chr6:69345129-69345140 chr6:69345027-69345036 chr6:69345146-69345157 chr6:69345354-69345361
11	UBTF	chr6:69344381-69345999	K562	blood:	n/a	n/a
12	POLR2A	chr6:69343604-69345662	H1-neurons	neurons:	n/a	n/a
13	CUX1	chr6:69344261-69344671	K562	blood:	n/a	n/a
14	RAD21	chr6:69344302-69344596	SK-N-SH_RA	brain:	n/a	n/a
15	ZNF384	chr6:69343863-69344643	K562	blood:	n/a	chr6:69344238-69344246
16	JUND	chr6:69343982-69345484	K562	blood:	n/a	chr6:69345026-69345035
17	REST	chr6:69344354-69344709	H1-hESC	embryonic stem cell:	n/a	n/a
18	GATA2	chr6:69343638-69344834	SH-SY5Y	brain:	n/a	n/a
19	IRF1	chr6:69344145-69344685	K562	blood:	n/a	chr6:69344619-69344633 chr6:69344650-69344659 chr6:69344334-69344345 chr6:69344333-69344347 chr6:69344623-69344633
20	CTBP2	chr6:69344295-69346023	H1-hESC	embryonic stem cell:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AL713998.1-2	chr6:69344357-69344616	NONHSAT113410
2	lnc-AL713998.1-2	chr6:69342555-69344919	ENSG00000230910.2
3	lnc-AL713998.1-2	chr6:69344077-69344611	NONHSAT113412
4	lnc-AL713998.1-2	chr6:69343940-69344888	NONHSAT113409
5	lnc-AL713998.1-2	chr6:69343940-69344888	NONHSAT113414
6	lnc-AL713998.1-2	chr6:69344077-69344985	NONHSAT113407
7	lnc-AL713998.1-2	chr6:69344357-69344616	NONHSAT113415
8	lnc-AL713998.1-2	chr6:69344077-69345052	NONHSAT113413
9	lnc-AL713998.1-2	chr6:69344357-69344967	NONHSAT113416

Variant related genes	Relation type
ENSG00000230910	TF binding region
BAI3	TF binding region

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1033520	0.85[JPT][hapmap]
rs10484791	0.85[CHB][hapmap];0.84[JPT][hapmap]
rs10945138	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs10945139	0.81[CEU][hapmap];0.85[CHB][hapmap];0.85[JPT][hapmap]
rs11752398	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs11752837	0.81[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap]
rs12154008	0.81[CEU][hapmap];0.85[CHB][hapmap];0.85[JPT][hapmap]
rs12201488	0.91[CHB][hapmap];0.90[JPT][hapmap]
rs12210045	0.90[CHB][hapmap]
rs13218712	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs2246093	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2246104	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2253759	0.90[JPT][hapmap]
rs2253866	0.85[CEU][hapmap];0.90[JPT][hapmap]
rs2254654	0.90[CHB][hapmap];0.94[JPT][hapmap]
rs2585592	0.85[JPT][hapmap]
rs2585597	0.86[JPT][hapmap]
rs2585598	0.85[JPT][hapmap]
rs2585599	0.85[CEU][hapmap];0.81[JPT][hapmap]
rs2585600	0.81[JPT][hapmap]
rs2585604	0.81[CEU][hapmap];0.81[JPT][hapmap]
rs2585614	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2585621	0.81[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap]
rs2585622	0.80[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap]
rs2585626	0.92[CEU][hapmap];0.90[JPT][hapmap];0.80[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs2585627	0.87[CEU][hapmap];0.90[JPT][hapmap];0.89[EUR][1000 genomes]
rs2746125	0.85[CEU][hapmap];0.90[JPT][hapmap]
rs2746127	0.85[CEU][hapmap];0.86[JPT][hapmap]
rs2746132	0.80[JPT][hapmap]
rs2746137	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs2746141	0.85[JPT][hapmap]
rs2802676	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs2802680	0.81[CEU][hapmap];0.81[JPT][hapmap]
rs2802683	0.81[JPT][hapmap]
rs2802684	0.84[CEU][hapmap];0.80[JPT][hapmap]
rs2802687	0.86[JPT][hapmap]
rs2802688	0.89[CEU][hapmap];0.86[JPT][hapmap]
rs2802689	0.89[JPT][hapmap]
rs2802691	0.84[CEU][hapmap];0.85[JPT][hapmap];0.82[EUR][1000 genomes]
rs2802692	0.89[EUR][1000 genomes]
rs2802693	0.90[JPT][hapmap];0.80[EUR][1000 genomes]
rs2802694	0.86[JPT][hapmap]
rs2802696	0.80[EUR][1000 genomes]
rs3121775	0.86[JPT][hapmap]
rs715294	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs7745837	0.91[CHB][hapmap];0.90[JPT][hapmap]
rs7768591	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs9360356	0.83[JPT][hapmap]
rs9791207	0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv886130	chr6:68950298-69531957	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv830680	chr6:69192214-69351103	Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	esv3340533	chr6:69343856-69346404	Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
4	esv3321603	chr6:69344081-69346129	Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:69342600-69349600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
2	chr6:69342600-69351000	Active TSS	Brain Angular Gyrus	brain
3	chr6:69342800-69348000	Active TSS	Fetal Brain Male	brain
4	chr6:69343000-69348000	Active TSS	Cortex derived primary cultured neurospheres	brain
5	chr6:69343200-69344400	Bivalent/Poised TSS	Fetal Lung	lung
6	chr6:69343200-69348600	Active TSS	Brain Cingulate Gyrus	brain
7	chr6:69343200-69348800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr6:69343200-69349200	Active TSS	Brain Germinal Matrix	brain
9	chr6:69343200-69351200	Active TSS	Brain Inferior Temporal Lobe	brain
10	chr6:69343200-69352000	Active TSS	Brain Anterior Caudate	brain
11	chr6:69343400-69348400	Active TSS	Fetal Stomach	stomach
12	chr6:69343400-69349600	Active TSS	Fetal Brain Female	brain
13	chr6:69343600-69344400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr6:69343600-69344800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr6:69343600-69345800	Bivalent/Poised TSS	Fetal Intestine Large	intestine
16	chr6:69343600-69345800	Active TSS	Rectal Smooth Muscle	rectum
17	chr6:69343600-69346200	Bivalent/Poised TSS	Fetal Intestine Small	intestine
18	chr6:69343600-69346400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr6:69343600-69346600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
20	chr6:69343600-69346800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
21	chr6:69343600-69347200	Active TSS	Duodenum Smooth Muscle	Duodenum
22	chr6:69343600-69347400	Active TSS	Brain Substantia Nigra	brain
23	chr6:69343600-69348200	Active TSS	Right Atrium	heart
24	chr6:69343800-69344400	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
25	chr6:69343800-69344400	Bivalent Enhancer	Primary B cells from peripheral blood	blood
26	chr6:69343800-69344400	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
27	chr6:69343800-69344400	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
28	chr6:69343800-69344400	Bivalent/Poised TSS	Primary mononuclear cells fromperipheralblood	Blood
29	chr6:69343800-69344400	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
30	chr6:69343800-69344800	Flanking Active TSS	Adipose Nuclei	Adipose
31	chr6:69343800-69345000	Active TSS	Colonic Mucosa	Colon
32	chr6:69343800-69345200	Active TSS	Skeletal Muscle Female	skeletal muscle
33	chr6:69343800-69345600	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
34	chr6:69343800-69345800	Flanking Active TSS	Liver	Liver
35	chr6:69343800-69346200	Bivalent/Poised TSS	Rectal Mucosa Donor 31	rectum
36	chr6:69343800-69346400	Active TSS	H9 Cell Line	embryonic stem cell
37	chr6:69343800-69346600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr6:69343800-69346600	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr6:69343800-69346600	Active TSS	Breast Myoepithelial Primary Cells	Breast
40	chr6:69343800-69346600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr6:69343800-69346600	Active TSS	Left Ventricle	heart
42	chr6:69343800-69346800	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
43	chr6:69343800-69346800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr6:69343800-69346800	Active TSS	Ovary	ovary
45	chr6:69343800-69347400	Active TSS	Colon Smooth Muscle	Colon
46	chr6:69344000-69344400	Bivalent Enhancer	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr6:69344000-69344400	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
48	chr6:69344000-69344400	Flanking Bivalent TSS/Enh	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr6:69344000-69344400	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
50	chr6:69344000-69344400	Active TSS	Primary T helper naive cells from peripheral blood	blood

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