Variant report

Variant	rs11683654
Chromosome Location	chr2:54276502-54276503
allele	A/G
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	FOXA1	chr2:54276381-54276809	HepG2	liver:	n/a	chr2:54276658-54276670 chr2:54276603-54276615
2	FOXA1	chr2:54276399-54276799	HepG2	liver:	n/a	chr2:54276658-54276670 chr2:54276603-54276615
3	FOXA1	chr2:54276335-54276768	HepG2	liver:	n/a	chr2:54276658-54276670 chr2:54276603-54276615
4	FOXA2	chr2:54276416-54276797	HepG2	liver:	n/a	chr2:54276658-54276670 chr2:54276603-54276615

Variant related genes	Relation type
HMGB1P31	TF binding region

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10084355	0.91[ASN][1000 genomes]
rs10201364	0.88[ASN][1000 genomes]
rs10865279	0.82[YRI][hapmap]
rs11125519	0.80[ASN][1000 genomes]
rs11687324	0.94[ASN][1000 genomes]
rs11695734	0.81[AMR][1000 genomes]
rs12713253	0.94[ASN][1000 genomes]
rs13414393	0.93[CHB][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs1363063	0.88[CHB][hapmap];0.83[JPT][hapmap];0.95[ASN][1000 genomes]
rs1421617	0.93[CHB][hapmap];0.83[JPT][hapmap];0.90[ASN][1000 genomes]
rs1559037	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs17045474	0.84[CEU][hapmap]
rs17045488	0.84[CEU][hapmap]
rs17268179	0.94[ASN][1000 genomes]
rs1833497	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs1862121	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs1862122	0.86[AMR][1000 genomes]
rs2111868	0.84[CHB][hapmap]
rs2884254	0.85[ASN][1000 genomes]
rs4671178	0.87[AMR][1000 genomes]
rs62140990	0.80[EUR][1000 genomes]
rs6545376	0.85[ASN][1000 genomes]
rs6749817	0.93[CHB][hapmap];0.89[ASN][1000 genomes]
rs718872	0.88[CHB][hapmap]
rs7558126	0.83[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs7569214	0.93[CHB][hapmap];0.84[ASN][1000 genomes]
rs7569370	0.93[CHB][hapmap];0.85[ASN][1000 genomes]
rs7571086	0.82[ASN][1000 genomes]
rs7576901	0.80[EUR][1000 genomes]
rs7590819	0.80[EUR][1000 genomes]
rs7590846	0.88[AMR][1000 genomes]
rs805308	0.94[CHB][hapmap]
rs805309	0.86[CHB][hapmap]
rs805322	0.86[CHB][hapmap]
rs805341	0.93[CHB][hapmap]
rs805360	0.93[CHB][hapmap]
rs805367	0.88[CHB][hapmap]
rs805374	0.86[CHB][hapmap]
rs805375	0.80[CHB][hapmap]
rs805410	0.86[CHB][hapmap]
rs805412	0.88[CHB][hapmap]
rs805423	0.86[CHB][hapmap]
rs805450	0.80[CHB][hapmap]
rs959286	0.83[YRI][hapmap]

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	nsv1001246	chr2:54195654-54434832	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
2	nsv1003205	chr2:54220049-54700843	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	esv2762639	chr2:54220049-54700855	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1011790	chr2:54220049-54714553	Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv1002891	chr2:54227005-54682169	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv535722	chr2:54227005-54682169	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
7	nsv1011690	chr2:54255361-54700843	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
8	nsv431069	chr2:54260132-54434049	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54248600-54278000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr2:54248600-54289800	Weak transcription	Fetal Lung	lung
3	chr2:54260400-54278200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr2:54266200-54281800	Weak transcription	Fetal Intestine Large	intestine
5	chr2:54268200-54282400	Weak transcription	Right Ventricle	heart
6	chr2:54268400-54286800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr2:54268400-54290800	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr2:54268800-54278200	Weak transcription	Pancreas	Pancrea
9	chr2:54270200-54276600	Weak transcription	Colon Smooth Muscle	Colon
10	chr2:54270400-54280200	Weak transcription	Ovary	ovary
11	chr2:54271200-54277000	Weak transcription	Aorta	Aorta
12	chr2:54271400-54286800	Weak transcription	HSMMtube	muscle
13	chr2:54271600-54278200	Weak transcription	Left Ventricle	heart
14	chr2:54271800-54278200	Weak transcription	Fetal Muscle Trunk	muscle
15	chr2:54271800-54281600	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr2:54272000-54280200	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr2:54272000-54280600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr2:54272000-54286600	Weak transcription	HSMM	muscle
19	chr2:54272200-54281600	Weak transcription	Brain Angular Gyrus	brain
20	chr2:54272200-54282800	Weak transcription	Brain Cingulate Gyrus	brain
21	chr2:54272400-54278200	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr2:54272600-54278200	Weak transcription	Adipose Nuclei	Adipose
23	chr2:54272600-54278200	Weak transcription	Liver	Liver
24	chr2:54272600-54278200	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr2:54272600-54278200	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr2:54272600-54279800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr2:54272600-54280000	Weak transcription	Primary hematopoietic stem cells	blood
28	chr2:54272600-54280000	Weak transcription	Brain Hippocampus Middle	brain
29	chr2:54272600-54280000	Weak transcription	Brain Substantia Nigra	brain
30	chr2:54272600-54280000	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr2:54272600-54280400	Weak transcription	Brain Germinal Matrix	brain
32	chr2:54272600-54286600	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr2:54272600-54286800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr2:54272800-54278000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr2:54272800-54278000	Weak transcription	Fetal Muscle Leg	muscle
36	chr2:54273000-54278400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr2:54273000-54292400	Weak transcription	Fetal Brain Female	brain
38	chr2:54273200-54276600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr2:54274800-54280600	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr2:54275200-54277200	Enhancers	HepG2	liver
41	chr2:54275200-54278000	Weak transcription	Fetal Intestine Small	intestine
42	chr2:54275200-54279800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr2:54275800-54277200	Enhancers	Stomach Smooth Muscle	stomach
44	chr2:54275800-54279800	Weak transcription	Osteobl	bone
45	chr2:54275800-54280000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr2:54275800-54280200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr2:54276000-54278200	Weak transcription	Primary B cells from cord blood	blood
48	chr2:54276000-54278400	Weak transcription	Primary T cells from cord blood	blood
49	chr2:54276000-54279600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr2:54276000-54280000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood

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