Variant report

Variant	rs59321237
Chromosome Location	chr6:101329742-101329743
allele	C/T
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	CHD1	chr6:101327624-101330167	IMR90	lung:	n/a	chr6:101329312-101329322
2	POLR2A	chr6:101328597-101329763	K562	blood:	n/a	n/a
3	SMC3	chr6:101328620-101330270	Hela-S3	cervix:	n/a	n/a
4	CCNT2	chr6:101328683-101329932	K562	blood:	n/a	chr6:101328716-101328725
5	POLR2A	chr6:101328647-101330043	GM12892	blood:	n/a	n/a
6	HMGN3	chr6:101328735-101329944	K562	blood:	n/a	n/a
7	TCF12	chr6:101328750-101329770	A549	lung:	n/a	chr6:101328877-101328887 chr6:101329000-101329007
8	IRF1	chr6:101328604-101330135	K562	blood:	n/a	chr6:101328614-101328628 chr6:101328999-101329013 chr6:101328998-101329010 chr6:101329305-101329319 chr6:101329005-101329019 chr6:101328823-101328832 chr6:101328997-101329017 chr6:101329762-101329772 chr6:101328861-101328875
9	SIN3AK20	chr6:101328717-101329779	HCT-116	colon:	n/a	n/a
10	E2F6	chr6:101328818-101329962	A549	lung:	n/a	chr6:101329287-101329296 chr6:101329369-101329379 chr6:101329109-101329124 chr6:101328865-101328874 chr6:101329209-101329219 chr6:101329312-101329323 chr6:101329306-101329315
11	TBP	chr6:101328954-101329770	Hela-S3	cervix:	n/a	n/a
12	JUND	chr6:101328330-101329834	K562	blood:	n/a	chr6:101329150-101329161
13	PML	chr6:101328921-101329848	K562	blood:	n/a	n/a
14	SETDB1	chr6:101328100-101330547	U2OS	brain:	n/a	n/a
15	POLR2A	chr6:101328602-101329813	PFSK-1	brain:	n/a	n/a
16	POLR2A	chr6:101328660-101330218	K562	blood:	n/a	n/a
17	ARID3A	chr6:101328160-101329909	HepG2	liver:	n/a	n/a
18	RELA	chr6:101328409-101329896	GM15510	blood:	n/a	n/a
19	GTF2F1	chr6:101329011-101330160	Hela-S3	cervix:	n/a	n/a
20	POLR2A	chr6:101328487-101330184	GM12878	blood:	n/a	n/a
21	POLR2A	chr6:101328101-101330072	MCF10A-Er-Src	breast:	n/a	n/a
22	POLR2A	chr6:101328554-101330124	PBDE	blood:	n/a	n/a
23	CHD1	chr6:101328502-101329815	GM12878	blood:	n/a	chr6:101329312-101329322
24	MAX	chr6:101328559-101329853	ECC-1	luminal epithelium:	n/a	chr6:101329314-101329324 chr6:101329135-101329142
25	WRNIP1	chr6:101328542-101330002	GM12878	blood:	n/a	n/a
26	CBX3	chr6:101328828-101329742	K562	blood:	n/a	n/a
27	E2F6	chr6:101328552-101330245	H1-hESC	embryonic stem cell:	n/a	chr6:101329287-101329296 chr6:101329369-101329379 chr6:101329109-101329124 chr6:101328865-101328874 chr6:101329209-101329219 chr6:101329312-101329323 chr6:101329306-101329315
28	CHD2	chr6:101328636-101329802	K562	blood:	n/a	chr6:101329312-101329322
29	POLR2A	chr6:101328352-101330058	Hela-S3	cervix:	n/a	n/a
30	MAX	chr6:101328362-101330089	NB4	blood:	n/a	chr6:101329314-101329324 chr6:101329135-101329142
31	POLR2A	chr6:101328347-101330202	MCF10A-Er-Src	breast:	n/a	n/a
32	RFX5	chr6:101328761-101330009	Hela-S3	cervix:	n/a	n/a
33	RAD21	chr6:101329239-101329765	HepG2	liver:	n/a	n/a
34	SMARCC1	chr6:101328780-101329843	Hela-S3	cervix:	n/a	n/a
35	ZKSCAN1	chr6:101329004-101330050	Hela-S3	cervix:	n/a	n/a
36	RELA	chr6:101328626-101330127	GM18951	blood:	n/a	n/a
37	POLR2A	chr6:101328730-101329809	GM12878	blood:	n/a	n/a
38	MAX	chr6:101328530-101329817	SK-N-SH	brain:	n/a	chr6:101329314-101329324 chr6:101329135-101329142
39	RAD21	chr6:101329189-101329756	H1-hESC	embryonic stem cell:	n/a	n/a
40	KAP1	chr6:101328380-101330607	HEK293	kidney:	n/a	n/a
41	HCFC1	chr6:101327729-101330325	Hela-S3	cervix:	n/a	n/a
42	GTF2F1	chr6:101329739-101330002	K562	blood:	n/a	n/a
43	MYC	chr6:101328408-101329936	A549	lung:	n/a	chr6:101329314-101329324 chr6:101329135-101329142
44	SIN3AK20	chr6:101328610-101329746	PANC-1	pancreas:	n/a	n/a
45	MXI1	chr6:101327954-101330323	SK-N-SH	brain:	n/a	n/a
46	MAFK	chr6:101328411-101329858	K562	blood:	n/a	n/a
47	UBTF	chr6:101328629-101329892	K562	blood:	n/a	n/a
48	POLR2A	chr6:101328338-101330279	HepG2	liver:	n/a	n/a
49	SIN3AK20	chr6:101328243-101329763	MCF-7	breast:	n/a	n/a
50	REST	chr6:101328546-101329842	H1-neurons	neurons:	n/a	chr6:101328975-101328988

No.	Distal block	Cell Line	Cell type
1	chr6:101327181..101330084-chr6:117801293..117803939,2	K562	blood:
2	chr6:101328677..101332841-chr6:101334376..101338552,5	K562	blood:
3	chr6:101326886..101330925-chr6:101337161..101339877,4	MCF-7	breast:
4	chr20:60970535..60972970-chr6:101328486..101330061,2	MCF-7	breast:
5	chr16:18801227..18802129-chr6:101329291..101329807,2	Hela-S3	cervix:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GRIK2-2	chr6:101329347-101330847	ENSG00000260000.1
2	lnc-GRIK2-2	chr6:101329347-101330863	ENSG00000260000.2

Variant related genes	Relation type
ASCC3	TF binding region
ENSG00000134419	Chromatin interaction
ENSG00000149679	Chromatin interaction
ENSG00000270987	Chromatin interaction
ENSG00000164465	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10485299	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11969893	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17054273	0.81[AFR][1000 genomes]
rs17061100	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17061214	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2201495	0.81[AFR][1000 genomes]
rs57169693	0.86[AFR][1000 genomes]
rs60569953	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6927313	0.81[AFR][1000 genomes]
rs72942985	0.83[AFR][1000 genomes]
rs72942988	0.83[AFR][1000 genomes]
rs72945134	0.81[AFR][1000 genomes]
rs72945178	0.88[AMR][1000 genomes]
rs72946452	0.87[EUR][1000 genomes]
rs72947044	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72947057	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9689068	0.81[AFR][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	nsv949535	chr6:100740293-101469052	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv1020692	chr6:101136992-101426071	ZNF genes & repeats Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv886457	chr6:101158950-101487473	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv1020400	chr6:101172705-101981665	Weak transcription Bivalent/Poised TSS Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv538390	chr6:101172705-101981665	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
6	nsv1019213	chr6:101225650-101623140	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
7	nsv538391	chr6:101225650-101623140	Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
8	esv2763587	chr6:101277874-101510491	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 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	chr6:101326600-101330200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr6:101327000-101329800	Active TSS	H1 Cell Line	embryonic stem cell
3	chr6:101327000-101330200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr6:101327200-101329800	Active TSS	iPS-15b Cell Line	embryonic stem cell
5	chr6:101327200-101330000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr6:101327400-101329800	Active TSS	HUES64 Cell Line	embryonic stem cell
7	chr6:101327400-101330200	Active TSS	A549	lung
8	chr6:101327400-101330200	Active TSS	HSMM	muscle
9	chr6:101327400-101330200	Active TSS	NHDF-Ad	bronchial
10	chr6:101327400-101330200	Active TSS	NHLF	lung
11	chr6:101327400-101330600	Active TSS	GM12878-XiMat	blood
12	chr6:101327400-101330800	Active TSS	ES-I3 Cell Line	embryonic stem cell
13	chr6:101327800-101329800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr6:101327800-101329800	Active TSS	HUES48 Cell Line	embryonic stem cell
15	chr6:101327800-101329800	Active TSS	Rectal Smooth Muscle	rectum
16	chr6:101327800-101330400	Active TSS	Rectal Mucosa Donor 29	rectum
17	chr6:101328000-101329800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr6:101328000-101329800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr6:101328000-101329800	Active TSS	Brain Angular Gyrus	brain
20	chr6:101328000-101329800	Active TSS	Brain Cingulate Gyrus	brain
21	chr6:101328000-101329800	Active TSS	Brain Inferior Temporal Lobe	brain
22	chr6:101328000-101329800	Active TSS	HMEC	breast
23	chr6:101328000-101329800	Active TSS	Osteobl	bone
24	chr6:101328000-101330000	Active TSS	Breast Myoepithelial Primary Cells	Breast
25	chr6:101328000-101330000	Active TSS	Brain Germinal Matrix	brain
26	chr6:101328000-101330000	Active TSS	K562	blood
27	chr6:101328000-101330200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
28	chr6:101328000-101330200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr6:101328000-101330200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr6:101328000-101330400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr6:101328200-101329800	Active TSS	HUES6 Cell Line	embryonic stem cell
32	chr6:101328200-101329800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr6:101328200-101329800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr6:101328200-101329800	Active TSS	Fetal Stomach	stomach
35	chr6:101328200-101329800	Active TSS	HSMMtube	muscle
36	chr6:101328200-101329800	Active TSS	NH-A	brain
37	chr6:101328200-101329800	Active TSS	NHEK	skin
38	chr6:101328200-101330000	Active TSS	Brain Hippocampus Middle	brain
39	chr6:101328200-101330000	Active TSS	Pancreatic Islets	Pancreatic Islet
40	chr6:101328200-101330000	Active TSS	Fetal Lung	lung
41	chr6:101328200-101330000	Active TSS	Ovary	ovary
42	chr6:101328200-101330000	Active TSS	Psoas Muscle	Psoas
43	chr6:101328200-101330000	Active TSS	Right Ventricle	heart
44	chr6:101328200-101330000	Active TSS	Stomach Mucosa	stomach
45	chr6:101328200-101330200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr6:101328200-101330200	Active TSS	Brain Substantia Nigra	brain
47	chr6:101328200-101330200	Active TSS	Stomach Smooth Muscle	stomach
48	chr6:101328400-101329800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr6:101328400-101329800	Active TSS	H9 Cell Line	embryonic stem cell
50	chr6:101328400-101329800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell

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