Variant report

Variant	rs3897906
Chromosome Location	chr3:101548610-101548611
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:31)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:31 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:101545970-101549723	GM12878	blood:	n/a	n/a
2	TBP	chr3:101547904-101549105	GM12878	blood:	n/a	n/a
3	WRNIP1	chr3:101547803-101548619	GM12878	blood:	n/a	n/a
4	TBL1XR1	chr3:101548054-101549038	GM12878	blood:	n/a	n/a
5	POLR2A	chr3:101547791-101548683	GM12892	blood:	n/a	n/a
6	CREB1	chr3:101547540-101549160	GM12878	blood:	n/a	n/a
7	EBF1	chr3:101547892-101549081	GM12878	blood:	n/a	n/a
8	RELA	chr3:101547855-101549010	GM18951	blood:	n/a	n/a
9	RUNX3	chr3:101547785-101549318	GM12878	blood:	n/a	n/a
10	POLR2A	chr3:101546020-101550047	GM12878	blood:	n/a	n/a
11	NFATC1	chr3:101548512-101549165	GM12878	blood:	n/a	n/a
12	BCLAF1	chr3:101547833-101548611	GM12878	blood:	n/a	n/a
13	POLR2A	chr3:101547122-101548611	GM12891	blood:	n/a	n/a
14	POLR2A	chr3:101546440-101549098	GM12891	blood:	n/a	n/a
15	POLR2A	chr3:101547708-101548662	GM12892	blood:	n/a	n/a
16	POLR2A	chr3:101547219-101548617	GM12892	blood:	n/a	n/a
17	POLR2A	chr3:101546013-101548953	GM18505	blood:	n/a	n/a
18	MTA3	chr3:101545885-101549139	GM12878	blood:	n/a	n/a
19	FOXM1	chr3:101548387-101549094	GM12878	blood:	n/a	n/a
20	PML	chr3:101547494-101549177	GM12878	blood:	n/a	n/a
21	POLR2A	chr3:101545998-101549072	GM12892	blood:	n/a	n/a
22	RELA	chr3:101547873-101549120	GM19099	blood:	n/a	n/a
23	POLR2A	chr3:101545992-101550685	GM12891	blood:	n/a	n/a
24	POLR2A	chr3:101545973-101549728	GM12878	blood:	n/a	n/a
25	NFIC	chr3:101547770-101549224	GM12878	blood:	n/a	n/a
26	NFIC	chr3:101548355-101549191	GM12878	blood:	n/a	n/a
27	STAT5A	chr3:101548270-101549028	GM12878	blood:	n/a	chr3:101548960-101548971
28	MTA3	chr3:101547863-101548673	GM12878	blood:	n/a	n/a
29	POLR2A	chr3:101547801-101549077	GM19099	blood:	n/a	n/a
30	CHD1	chr3:101546026-101549293	GM12878	blood:	n/a	n/a
31	ATF2	chr3:101547628-101549193	GM12878	blood:	n/a	chr3:101547730-101547737

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:101548022..101550222-chr3:101553526..101557259,3	K562	blood:
2	chr3:101543921..101548093-chr3:101548561..101552657,6	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:
6	chr3:101547198..101549505-chr3:101556556..101560053,3	MCF-7	breast:

No data

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

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs11708277	1.00[LWK][hapmap]
rs13322146	1.00[CEU][hapmap]
rs2114302	1.00[LWK][hapmap]
rs2449495	1.00[LWK][hapmap]
rs9873837	1.00[CEU][hapmap]

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:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:101545600-101549200	Active TSS	Breast Myoepithelial Primary Cells	Breast
2	chr3:101546800-101553000	Weak transcription	Spleen	Spleen
3	chr3:101547000-101549200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
4	chr3:101547000-101552400	Weak transcription	Fetal Brain Female	brain
5	chr3:101547000-101561000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr3:101547200-101549000	Enhancers	Skeletal Muscle Male	skeletal muscle
7	chr3:101547400-101548800	Flanking Active TSS	Colon Smooth Muscle	Colon
8	chr3:101547400-101549000	Enhancers	Primary neutrophils fromperipheralblood	blood
9	chr3:101547400-101549000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
10	chr3:101547400-101549000	Enhancers	Brain Substantia Nigra	brain
11	chr3:101547400-101549400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
12	chr3:101547600-101548800	Enhancers	Primary hematopoietic stem cells short term culture	blood
13	chr3:101547600-101548800	Enhancers	Cortex derived primary cultured neurospheres	brain
14	chr3:101547600-101548800	Enhancers	Brain Angular Gyrus	brain
15	chr3:101547600-101549000	Enhancers	Primary T cells from cord blood	blood
16	chr3:101547600-101549000	Enhancers	Brain Anterior Caudate	brain
17	chr3:101547800-101548800	Enhancers	Primary hematopoietic stem cells	blood
18	chr3:101547800-101548800	Enhancers	Sigmoid Colon	Sigmoid Colon
19	chr3:101547800-101549000	Flanking Active TSS	Stomach Smooth Muscle	stomach
20	chr3:101547800-101549400	Enhancers	Small Intestine	intestine
21	chr3:101548000-101549000	Enhancers	Primary T cells fromperipheralblood	blood
22	chr3:101548000-101549400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
23	chr3:101548000-101549400	Enhancers	Ovary	ovary
24	chr3:101548000-101549600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
25	chr3:101548000-101550800	Enhancers	Primary monocytes fromperipheralblood	blood
26	chr3:101548200-101549000	Enhancers	Brain Hippocampus Middle	brain
27	chr3:101548200-101549200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
28	chr3:101548200-101550600	Enhancers	Primary B cells from peripheral blood	blood
29	chr3:101548200-101551800	Weak transcription	Psoas Muscle	Psoas
30	chr3:101548200-101552000	Weak transcription	Pancreas	Pancrea
31	chr3:101548200-101552400	Weak transcription	Right Atrium	heart
32	chr3:101548200-101552400	Weak transcription	K562	blood
33	chr3:101548200-101552600	Weak transcription	Colonic Mucosa	Colon
34	chr3:101548200-101560800	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr3:101548200-101560800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr3:101548200-101565600	Weak transcription	Lung	lung
37	chr3:101548400-101548800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr3:101548400-101548800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr3:101548400-101548800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
40	chr3:101548400-101549000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
41	chr3:101548400-101549000	Enhancers	Primary T killer memory cells from peripheral blood	blood
42	chr3:101548400-101549000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr3:101548400-101549000	Enhancers	Liver	Liver
44	chr3:101548400-101549000	Enhancers	Fetal Lung	lung
45	chr3:101548400-101549200	Enhancers	Primary B cells from cord blood	blood
46	chr3:101548400-101549200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
47	chr3:101548400-101549200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr3:101548400-101549200	Enhancers	Muscle Satellite Cultured Cells	--
49	chr3:101548400-101549200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr3:101548400-101549600	Enhancers	Primary T helper naive cells from peripheral blood	blood

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