Variant report

Variant	rs10880935
Chromosome Location	chr12:46595290-46595291
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:37)
CpG islands
(count:0)
Chromatin interactive
region (count:20)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:37 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	REST	chr12:46595126-46595682	MCF-7	breast:	n/a	chr12:46595165-46595185
2	RAD21	chr12:46594905-46595715	MCF-7	breast:	n/a	n/a
3	REST	chr12:46595205-46595390	H1-hESC	embryonic stem cell:	n/a	n/a
4	JUND	chr12:46594968-46595708	T-47D	breast:	n/a	n/a
5	SIN3AK20	chr12:46594933-46595878	MCF-7	breast:	n/a	n/a
6	POLR2A	chr12:46595288-46595326	MCF-7	breast:	n/a	n/a
7	ESR1	chr12:46594979-46595756	T-47D	breast:	n/a	n/a
8	ESR1	chr12:46595045-46595745	T-47D	breast:	n/a	n/a
9	ZNF217	chr12:46595018-46595693	MCF-7	breast:	n/a	n/a
10	TCF7L2	chr12:46595132-46595625	MCF-7	breast:	n/a	n/a
11	EP300	chr12:46595026-46595848	MCF-7	breast:	n/a	n/a
12	RAD21	chr12:46595013-46595774	MCF-7	breast:	n/a	n/a
13	POLR2A	chr12:46595271-46595523	GM12891	blood:	n/a	n/a
14	GATA3	chr12:46594970-46595769	MCF-7	breast:	n/a	n/a
15	FOXM1	chr12:46595142-46595782	MCF-7	breast:	n/a	n/a
16	POLR2A	chr12:46595290-46595683	Hela-S3	cervix:	n/a	n/a
17	ESR1	chr12:46595036-46595749	T-47D	breast:	n/a	n/a
18	ESR1	chr12:46595079-46595744	T-47D	breast:	n/a	n/a
19	GATA3	chr12:46594996-46595839	MCF-7	breast:	n/a	n/a
20	TCF12	chr12:46595048-46596080	MCF-7	breast:	n/a	n/a
21	GATA3	chr12:46595006-46595556	T-47D	breast:	n/a	n/a
22	FOXA1	chr12:46595124-46595506	T-47D	breast:	n/a	n/a
23	TEAD4	chr12:46595069-46595723	MCF-7	breast:	n/a	n/a
24	HDAC2	chr12:46595034-46595725	MCF-7	breast:	n/a	n/a
25	GATA3	chr12:46595091-46595696	MCF-7	breast:	n/a	n/a
26	ESR1	chr12:46595059-46595679	T-47D	breast:	n/a	n/a
27	FOXM1	chr12:46595062-46595881	MCF-7	breast:	n/a	n/a
28	POLR2A	chr12:46595087-46595611	K562	blood:	n/a	n/a
29	SIN3AK20	chr12:46594836-46595950	MCF-7	breast:	n/a	n/a
30	HDAC2	chr12:46594990-46595753	MCF-7	breast:	n/a	n/a
31	GATA3	chr12:46594691-46595875	MCF-7	breast:	n/a	n/a
32	NR2F2	chr12:46594998-46595798	MCF-7	breast:	n/a	n/a
33	NR2F2	chr12:46594973-46595779	MCF-7	breast:	n/a	n/a
34	EP300	chr12:46594921-46595831	MCF-7	breast:	n/a	n/a
35	GATA3	chr12:46595027-46595538	T-47D	breast:	n/a	n/a
36	TEAD4	chr12:46595178-46595724	MCF-7	breast:	n/a	n/a
37	TCF12	chr12:46595011-46595724	MCF-7	breast:	n/a	n/a

No data

(count:20 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:46594018..46595589-chr12:46607085..46608611,2	K562	blood:
2	chr12:46588900..46591153-chr12:46593120..46595375,3	MCF-7	breast:
3	chr12:46573159..46574150-chr12:46595090..46595990,8	MCF-7	breast:
4	chr12:46590374..46592807-chr12:46594598..46596416,2	K562	blood:
5	chr12:46593182..46595515-chr12:46654279..46656070,2	MCF-7	breast:
6	chr12:46593741..46596593-chr12:46600786..46603136,2	MCF-7	breast:
7	chr12:46573159..46574036-chr12:46595074..46595990,6	MCF-7	breast:
8	chr12:46595062..46596035-chr12:46887567..46888241,2	MCF-7	breast:
9	chr12:46381552..46382503-chr12:46595173..46595922,2	MCF-7	breast:
10	chr12:46580626..46582409-chr12:46594371..46596470,2	K562	blood:
11	chr12:46593049..46595554-chr12:46612027..46614436,2	MCF-7	breast:
12	chr12:46593719..46596069-chr12:46598625..46601594,2	K562	blood:
13	chr12:46593902..46597897-chr12:46605177..46609280,4	MCF-7	breast:
14	chr12:46595247..46598167-chr12:46765008..46767085,2	MCF-7	breast:
15	chr12:46590494..46598595-chr12:46658954..46664180,10	MCF-7	breast:
16	chr12:46593439..46596072-chr12:46660692..46663699,3	MCF-7	breast:
17	chr12:46553848..46555931-chr12:46593507..46596350,2	MCF-7	breast:
18	chr12:46590374..46592185-chr12:46593694..46596416,2	K562	blood:
19	chr12:46595186..46598496-chr12:46654294..46656727,3	MCF-7	breast:
20	chr12:46571164..46575821-chr12:46593446..46599247,7	MCF-7	breast:

No data

Variant related genes	Relation type
SLC38A1	TF binding region
ENSG00000258096	Chromatin interaction
ENSG00000134294	Chromatin interaction
ENSG00000111371	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11183394	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11608815	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11615731	1.00[CHB][hapmap]
rs12299972	0.96[ASN][1000 genomes]
rs12422328	0.80[ASN][1000 genomes]
rs1444590	1.00[CHB][hapmap]
rs2289769	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs61923106	0.92[ASN][1000 genomes]
rs6582621	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7133522	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7980700	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv826360	chr12:46515374-46598243	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	esv2754441	chr12:46590364-46605239	Strong transcription ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:46581600-46603200	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr12:46582200-46603200	Weak transcription	Small Intestine	intestine
3	chr12:46586800-46595400	Strong transcription	Placenta	Placenta
4	chr12:46587400-46602000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr12:46587400-46602000	Strong transcription	Muscle Satellite Cultured Cells	--
6	chr12:46587400-46603000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr12:46587800-46601400	Strong transcription	HSMMtube	muscle
8	chr12:46588000-46598600	Strong transcription	Primary B cells from peripheral blood	blood
9	chr12:46588000-46603000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr12:46588200-46598600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr12:46588200-46598800	Strong transcription	Primary T helper cells PMA-I stimulated	--
12	chr12:46588200-46598800	Strong transcription	Primary T helper cells fromperipheralblood	blood
13	chr12:46588200-46601200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr12:46588200-46601400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr12:46588200-46602200	Strong transcription	HUVEC	blood vessel
16	chr12:46588400-46599800	Strong transcription	Primary T cells from cord blood	blood
17	chr12:46588400-46600400	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr12:46588400-46601400	Strong transcription	Rectal Mucosa Donor 29	rectum
19	chr12:46588400-46602200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr12:46588400-46602400	Strong transcription	HMEC	breast
21	chr12:46588600-46595800	Strong transcription	Fetal Brain Female	brain
22	chr12:46588600-46598800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr12:46588600-46601400	Strong transcription	Duodenum Mucosa	Duodenum
24	chr12:46588600-46602000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
25	chr12:46588600-46602400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr12:46588600-46602800	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr12:46588800-46598600	Strong transcription	Primary T helper naive cells from peripheral blood	blood
28	chr12:46588800-46601600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr12:46588800-46602000	Strong transcription	HepG2	liver
30	chr12:46588800-46602400	Strong transcription	Rectal Mucosa Donor 31	rectum
31	chr12:46589000-46601400	Strong transcription	Sigmoid Colon	Sigmoid Colon
32	chr12:46589000-46601600	Strong transcription	HSMM	muscle
33	chr12:46589400-46602400	Strong transcription	Primary T cells fromperipheralblood	blood
34	chr12:46589600-46603000	Strong transcription	NHEK	skin
35	chr12:46589800-46608400	Weak transcription	Primary monocytes fromperipheralblood	blood
36	chr12:46590200-46600000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr12:46590200-46601200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr12:46590600-46599600	Strong transcription	Primary B cells from cord blood	blood
39	chr12:46590600-46601200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr12:46590600-46601600	Strong transcription	Primary hematopoietic stem cells	blood
41	chr12:46590600-46601800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr12:46590600-46602000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr12:46590600-46603200	Weak transcription	Pancreas	Pancrea
44	chr12:46590600-46603200	Weak transcription	Right Atrium	heart
45	chr12:46590600-46603600	Weak transcription	Brain Angular Gyrus	brain
46	chr12:46590600-46603800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr12:46590800-46601400	Strong transcription	A549	lung
48	chr12:46590800-46601600	Strong transcription	ES-I3 Cell Line	embryonic stem cell
49	chr12:46590800-46601600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
50	chr12:46590800-46603000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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