Variant report

Variant	rs73431965
Chromosome Location	chr6:49517951-49517952
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:41)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:41 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr6:49517755-49519554	HCT-116	colon:	n/a	chr6:49518356-49518363
2	MAX	chr6:49517644-49519344	H1-hESC	embryonic stem cell:	n/a	chr6:49518356-49518363
3	POLR2A	chr6:49517816-49519779	SK-N-MC	brain:	n/a	n/a
4	POLR2A	chr6:49517756-49519681	H1-hESC	embryonic stem cell:	n/a	n/a
5	TAF1	chr6:49517776-49518762	H1-hESC	embryonic stem cell:	n/a	n/a
6	HA-E2F1	chr6:49517738-49519388	MCF-7	breast:	n/a	n/a
7	CHD1	chr6:49517877-49518628	H1-hESC	embryonic stem cell:	n/a	n/a
8	SIN3A	chr6:49517827-49519792	H1-hESC	embryonic stem cell:	n/a	n/a
9	ZNF263	chr6:49517770-49519815	HEK293-T-REx	kidney:	n/a	chr6:49518987-49519008
10	POLR2A	chr6:49517940-49518154	ProgFib	skin:	n/a	n/a
11	E2F6	chr6:49517622-49519321	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr6:49517913-49518611	MCF10A-Er-Src	breast:	n/a	n/a
13	CTBP2	chr6:49517789-49519491	H1-hESC	embryonic stem cell:	n/a	n/a
14	MAX	chr6:49517624-49519414	H1-hESC	embryonic stem cell:	n/a	chr6:49518356-49518363
15	ZNF143	chr6:49517701-49519549	H1-hESC	embryonic stem cell:	n/a	n/a
16	MAX	chr6:49517734-49519487	H1-hESC	embryonic stem cell:	n/a	chr6:49518356-49518363
17	MAX	chr6:49517923-49518755	HCT-116	colon:	n/a	chr6:49518356-49518363
18	JUND	chr6:49517854-49518883	H1-hESC	embryonic stem cell:	n/a	n/a
19	TCF12	chr6:49517641-49518011	H1-hESC	embryonic stem cell:	n/a	n/a
20	POLR2A	chr6:49517634-49519474	H1-hESC	embryonic stem cell:	n/a	n/a
21	E2F6	chr6:49517510-49519567	H1-hESC	embryonic stem cell:	n/a	n/a
22	MAX	chr6:49517887-49519342	A549	lung:	n/a	chr6:49518356-49518363
23	POLR2A	chr6:49517623-49519307	MCF-7	breast:	n/a	n/a
24	SP1	chr6:49517701-49518487	H1-hESC	embryonic stem cell:	n/a	n/a
25	CHD2	chr6:49517847-49519023	H1-hESC	embryonic stem cell:	n/a	n/a
26	TAF1	chr6:49517711-49519429	H1-hESC	embryonic stem cell:	n/a	n/a
27	POLR2A	chr6:49517622-49519547	H1-hESC	embryonic stem cell:	n/a	n/a
28	POLR2A	chr6:49517717-49518014	H1-hESC	embryonic stem cell:	n/a	n/a
29	SIN3AK20	chr6:49517764-49519402	MCF-7	breast:	n/a	n/a
30	TAF1	chr6:49517925-49518733	MCF-7	breast:	n/a	n/a
31	TCF12	chr6:49517897-49519335	A549	lung:	n/a	n/a
32	GTF2F1	chr6:49517829-49519427	H1-hESC	embryonic stem cell:	n/a	n/a
33	SIN3AK20	chr6:49517749-49519895	MCF-7	breast:	n/a	n/a
34	MYC	chr6:49517808-49519151	H1-hESC	embryonic stem cell:	n/a	chr6:49518356-49518363
35	TBP	chr6:49517734-49519568	H1-hESC	embryonic stem cell:	n/a	n/a
36	GATA3	chr6:49517782-49518755	MCF-7	breast:	n/a	n/a
37	PML	chr6:49517944-49518692	MCF-7	breast:	n/a	n/a
38	YY1	chr6:49517759-49518542	H1-hESC	embryonic stem cell:	n/a	n/a
39	TCF12	chr6:49517700-49518102	H1-hESC	embryonic stem cell:	n/a	n/a
40	POLR2A	chr6:49517808-49519323	MCF-7	breast:	n/a	n/a
41	KAP1	chr6:49517941-49519534	HEK293	kidney:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:49515017..49518306-chr6:49519777..49524035,4	K562	blood:
2	chr6:49429390..49432411-chr6:49516710..49519961,3	MCF-7	breast:

No data

Variant related genes	Relation type
C6orf141	TF binding region
ENSG00000031691	Chromatin interaction
ENSG00000146085	Chromatin interaction
ENSG00000197261	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10456625	1.00[EUR][1000 genomes]
rs41273692	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41273694	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs45551532	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6458697	1.00[EUR][1000 genomes]
rs6905369	1.00[EUR][1000 genomes]
rs6912159	1.00[EUR][1000 genomes]
rs6912178	1.00[EUR][1000 genomes]
rs6912690	1.00[EUR][1000 genomes]
rs6919458	1.00[EUR][1000 genomes]
rs6925445	1.00[EUR][1000 genomes]
rs6927176	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6927459	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6939453	1.00[EUR][1000 genomes]
rs6939457	1.00[EUR][1000 genomes]
rs73431999	1.00[EUR][1000 genomes]
rs73433806	1.00[EUR][1000 genomes]
rs73433809	1.00[EUR][1000 genomes]
rs73433816	1.00[EUR][1000 genomes]
rs7742891	1.00[EUR][1000 genomes]
rs7758141	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7760893	1.00[EUR][1000 genomes]
rs7761036	1.00[EUR][1000 genomes]
rs7761928	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9349495	1.00[EUR][1000 genomes]
rs9473590	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024959	chr6:49290141-49652124	Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv1021136	chr6:49295037-49631278	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv885881	chr6:49439805-49575141	Weak transcription Bivalent Enhancer Strong transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv933942	chr6:49480550-50004231	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
5	nsv933833	chr6:49515134-49961765	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:49517400-49518000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr6:49517400-49519800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
3	chr6:49517400-49520000	Active TSS	iPS-18 Cell Line	embryonic stem cell
4	chr6:49517400-49520000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
5	chr6:49517600-49518000	Active TSS	H1 Cell Line	embryonic stem cell
6	chr6:49517600-49518000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr6:49517600-49518000	Bivalent/Poised TSS	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr6:49517600-49519800	Active TSS	Breast Myoepithelial Primary Cells	Breast
9	chr6:49517800-49518000	Active TSS	H9 Cell Line	embryonic stem cell
10	chr6:49517800-49518000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
11	chr6:49517800-49518000	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
12	chr6:49517800-49518000	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr6:49517800-49518000	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr6:49517800-49518000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr6:49517800-49518000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr6:49517800-49518000	Flanking Active TSS	Adipose Nuclei	Adipose
17	chr6:49517800-49518000	Enhancers	Liver	Liver
18	chr6:49517800-49518000	Active TSS	Brain Hippocampus Middle	brain
19	chr6:49517800-49518000	Active TSS	Duodenum Smooth Muscle	Duodenum
20	chr6:49517800-49518000	Bivalent Enhancer	Fetal Brain Female	brain
21	chr6:49517800-49518000	Flanking Active TSS	Fetal Intestine Small	intestine
22	chr6:49517800-49518000	Enhancers	Placenta	Placenta
23	chr6:49517800-49518000	Bivalent/Poised TSS	Fetal Stomach	stomach
24	chr6:49517800-49518000	Enhancers	Pancreas	Pancrea
25	chr6:49517800-49518000	Enhancers	Placenta Amnion	Placenta Amnion
26	chr6:49517800-49518000	Active TSS	Rectal Mucosa Donor 29	rectum
27	chr6:49517800-49518000	Active TSS	Rectal Mucosa Donor 31	rectum
28	chr6:49517800-49518000	Enhancers	Right Atrium	heart
29	chr6:49517800-49518000	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
30	chr6:49517800-49518000	Active TSS	Stomach Mucosa	stomach
31	chr6:49517800-49518000	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
32	chr6:49517800-49518000	Active TSS	NH-A	brain
33	chr6:49517800-49518200	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr6:49517800-49518200	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
35	chr6:49517800-49518200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr6:49517800-49518200	Bivalent/Poised TSS	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr6:49517800-49518200	Active TSS	Duodenum Mucosa	Duodenum
38	chr6:49517800-49518200	Active TSS	Right Ventricle	heart
39	chr6:49517800-49518200	Flanking Active TSS	HMEC	breast
40	chr6:49517800-49518200	Flanking Bivalent TSS/Enh	HUVEC	blood vessel
41	chr6:49517800-49518200	Flanking Active TSS	NHEK	skin
42	chr6:49517800-49518400	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
43	chr6:49517800-49518400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr6:49517800-49518400	Flanking Bivalent TSS/Enh	Fetal Lung	lung
45	chr6:49517800-49518800	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr6:49517800-49518800	Active TSS	Pancreatic Islets	Pancreatic Islet
47	chr6:49517800-49519000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
48	chr6:49517800-49519000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr6:49517800-49519000	Active TSS	Brain Anterior Caudate	brain
50	chr6:49517800-49519200	Bivalent/Poised TSS	Fetal Intestine Large	intestine

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