Variant report

Variant	rs665631
Chromosome Location	chr3:101547139-101547140
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:72)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:72 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr3:101546208-101547169	HepG2	liver:	n/a	n/a
2	POLR2A	chr3:101545970-101549723	GM12878	blood:	n/a	n/a
3	SP1	chr3:101545997-101547148	HCT-116	colon:	n/a	n/a
4	MYC	chr3:101546141-101547459	MCF10A-Er-Src	breast:	n/a	n/a
5	EP300	chr3:101546287-101547349	GM12878	blood:	n/a	chr3:101547083-101547097 chr3:101547080-101547094 chr3:101547079-101547093 chr3:101547248-101547258
6	POLR2A	chr3:101546323-101547169	U87	brain:	n/a	n/a
7	POLR2A	chr3:101546474-101547569	GM12891	blood:	n/a	n/a
8	EP300	chr3:101546036-101547409	GM12878	blood:	n/a	chr3:101547083-101547097 chr3:101547080-101547094 chr3:101547079-101547093 chr3:101547248-101547258
9	TEAD4	chr3:101546570-101547157	K562	blood:	n/a	n/a
10	RELA	chr3:101546149-101547250	GM12878	blood:	n/a	n/a
11	RUNX3	chr3:101546027-101547307	GM12878	blood:	n/a	n/a
12	CREB1	chr3:101546036-101547529	GM12878	blood:	n/a	n/a
13	POLR2A	chr3:101546491-101547421	GM12878	blood:	n/a	n/a
14	POLR2A	chr3:101546089-101547478	GM12878	blood:	n/a	n/a
15	ATF2	chr3:101545927-101547466	GM12878	blood:	n/a	n/a
16	PML	chr3:101545891-101547270	GM12878	blood:	n/a	n/a
17	MAX	chr3:101546187-101547161	A549	lung:	n/a	n/a
18	POLR2A	chr3:101546020-101550047	GM12878	blood:	n/a	n/a
19	NFIC	chr3:101545697-101547640	GM12878	blood:	n/a	n/a
20	MAX	chr3:101546065-101547158	HCT-116	colon:	n/a	n/a
21	ATF2	chr3:101545940-101547176	GM12878	blood:	n/a	n/a
22	POLR2A	chr3:101545966-101548189	MCF10A-Er-Src	breast:	n/a	n/a
23	POLR2A	chr3:101547122-101548611	GM12891	blood:	n/a	n/a
24	NFATC1	chr3:101546194-101547392	GM12878	blood:	n/a	n/a
25	STAT3	chr3:101546119-101547327	GM12878	blood:	n/a	n/a
26	POLR2A	chr3:101546010-101547600	GM19099	blood:	n/a	n/a
27	POLR2A	chr3:101546515-101547173	GM12892	blood:	n/a	n/a
28	BCLAF1	chr3:101545994-101547465	GM12878	blood:	n/a	n/a
29	CUX1	chr3:101546131-101547423	GM12878	blood:	n/a	n/a
30	MYC	chr3:101546421-101547229	K562	blood:	n/a	n/a
31	POLR2A	chr3:101546440-101549098	GM12891	blood:	n/a	n/a
32	BCL3	chr3:101546355-101547218	A549	lung:	n/a	n/a
33	NFIC	chr3:101545857-101547391	GM12878	blood:	n/a	n/a
34	POLR2A	chr3:101546415-101547506	GM18951	blood:	n/a	n/a
35	TCF7L2	chr3:101546257-101547450	HEK293	kidney:	n/a	n/a
36	NFATC1	chr3:101546056-101547494	GM12878	blood:	n/a	n/a
37	MTA3	chr3:101545954-101547542	GM12878	blood:	n/a	n/a
38	RCOR1	chr3:101546053-101547206	GM12878	blood:	n/a	n/a
39	MAZ	chr3:101546030-101547503	GM12878	blood:	n/a	n/a
40	RELA	chr3:101546069-101547148	GM18951	blood:	n/a	n/a
41	TBP	chr3:101546024-101547477	GM12878	blood:	n/a	n/a
42	POLR2A	chr3:101546030-101548421	GM12878	blood:	n/a	n/a
43	RELA	chr3:101546287-101547406	GM12892	blood:	n/a	n/a
44	E2F6	chr3:101546322-101547155	A549	lung:	n/a	n/a
45	FOXM1	chr3:101546200-101547212	GM12878	blood:	n/a	n/a
46	POLR2A	chr3:101546095-101547471	GM19193	blood:	n/a	n/a
47	POLR2A	chr3:101546021-101547176	H1-hESC	embryonic stem cell:	n/a	n/a
48	POLR2A	chr3:101546013-101548953	GM18505	blood:	n/a	n/a
49	MTA3	chr3:101545885-101549139	GM12878	blood:	n/a	n/a
50	IRF1	chr3:101546701-101547273	K562	blood:	n/a	chr3:101547088-101547102

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:101547017..101548528-chr3:101567687..101569494,2	K562	blood:
2	chr3:101546905..101548407-chr3:101551219..101553044,2	MCF-7	breast:
3	chr20:45943137..45945781-chr3:101546721..101548950,2	MCF-7	breast:
4	chr3:101543661..101554550-chr3:101566310..101574179,30	MCF-7	breast:
5	chr3:101544475..101550800-chr3:101565965..101572617,10	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FAM55C-1	chr3:101547088-101547652	NONHSAT090913

No data

Variant related genes	Relation type
ENSG00000249474	TF binding region
ENSG00000263770	Chromatin interaction
ENSG00000144802	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs2466369	1.00[MEX][hapmap]
rs2611836	1.00[MEX][hapmap]
rs2611840	0.82[EUR][1000 genomes]
rs2625282	1.00[MEX][hapmap]
rs2625283	1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs2625289	1.00[MEX][hapmap]
rs2722162	0.82[EUR][1000 genomes]
rs3821727	1.00[CHB][hapmap]
rs605621	1.00[ASN][1000 genomes]
rs623753	1.00[ASN][1000 genomes]
rs682610	1.00[EUR][1000 genomes];1.00[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	nsv497784	chr3:101315009-102092989	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv997407	chr3:101384031-101611391	Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
3	nsv536675	chr3:101384031-101611391	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats 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	76 gene(s)	inside rSNPs	diseases
4	esv3351469	chr3:101511702-101866448	Weak transcription Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:101539800-101548000	Weak transcription	Hela-S3	cervix
2	chr3:101541000-101548000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:101545600-101549200	Active TSS	Breast Myoepithelial Primary Cells	Breast
4	chr3:101546000-101547200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr3:101546000-101547200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr3:101546000-101547200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr3:101546000-101547200	Active TSS	Primary T helper naive cells from peripheral blood	blood
8	chr3:101546000-101547200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr3:101546000-101547200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
10	chr3:101546000-101547200	Active TSS	Duodenum Mucosa	Duodenum
11	chr3:101546000-101547200	Active TSS	Fetal Intestine Large	intestine
12	chr3:101546000-101547200	Active TSS	Fetal Intestine Small	intestine
13	chr3:101546000-101547200	Active TSS	Pancreatic Islets	Pancreatic Islet
14	chr3:101546000-101547200	Active TSS	Fetal Lung	lung
15	chr3:101546000-101547200	Active TSS	Fetal Muscle Leg	muscle
16	chr3:101546000-101547200	Active TSS	Fetal Stomach	stomach
17	chr3:101546000-101547200	Active TSS	Rectal Mucosa Donor 31	rectum
18	chr3:101546000-101547200	Active TSS	Rectal Smooth Muscle	rectum
19	chr3:101546000-101547200	Active TSS	Right Ventricle	heart
20	chr3:101546000-101547200	Active TSS	Skeletal Muscle Male	skeletal muscle
21	chr3:101546000-101547200	Active TSS	HepG2	liver
22	chr3:101546000-101547200	Active TSS	NHDF-Ad	bronchial
23	chr3:101546000-101547200	Active TSS	NHEK	skin
24	chr3:101546000-101547200	Active TSS	Osteobl	bone
25	chr3:101546000-101547400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr3:101546000-101547400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
27	chr3:101546000-101547400	Active TSS	Colonic Mucosa	Colon
28	chr3:101546000-101547400	Active TSS	Colon Smooth Muscle	Colon
29	chr3:101546000-101547400	Active TSS	Fetal Kidney	kidney
30	chr3:101546000-101547400	Active TSS	Thymus	Thymus
31	chr3:101546000-101547400	Active TSS	A549	lung
32	chr3:101546000-101547400	Flanking Active TSS	HUVEC	blood vessel
33	chr3:101546000-101547600	Active TSS	ES-I3 Cell Line	embryonic stem cell
34	chr3:101546000-101547600	Active TSS	iPS-20b Cell Line	embryonic stem cell
35	chr3:101546000-101547600	Flanking Active TSS	Primary T cells from cord blood	blood
36	chr3:101546000-101547600	Active TSS	Psoas Muscle	Psoas
37	chr3:101546000-101547800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr3:101546000-101547800	Flanking Active TSS	Primary hematopoietic stem cells	blood
39	chr3:101546000-101547800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr3:101546000-101547800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr3:101546000-101547800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr3:101546000-101547800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr3:101546000-101547800	Active TSS	Rectal Mucosa Donor 29	rectum
44	chr3:101546000-101547800	Active TSS	Right Atrium	heart
45	chr3:101546000-101547800	Active TSS	Stomach Smooth Muscle	stomach
46	chr3:101546000-101547800	Active TSS	HSMM	muscle
47	chr3:101546000-101547800	Active TSS	HSMMtube	muscle
48	chr3:101546000-101548000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
49	chr3:101546000-101548200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr3:101546000-101548200	Active TSS	Aorta	Aorta

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