Variant report

Variant	rs17268200
Chromosome Location	chr2:54281851-54281852
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:54196632..54198799-chr2:54280134..54282598,3	MCF-7	breast:
2	chr2:54196526..54198487-chr2:54280269..54283258,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000170634	Chromatin interaction
ENSG00000068878	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs11892920	1.00[CHB][hapmap]
rs1363061	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1727505	1.00[CHB][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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17268200	HMGB1P31	cis	Muscle Skeletal	GTEx

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54248600-54289800	Weak transcription	Fetal Lung	lung
2	chr2:54268200-54282400	Weak transcription	Right Ventricle	heart
3	chr2:54268400-54286800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr2:54268400-54290800	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr2:54271400-54286800	Weak transcription	HSMMtube	muscle
6	chr2:54272000-54286600	Weak transcription	HSMM	muscle
7	chr2:54272200-54282800	Weak transcription	Brain Cingulate Gyrus	brain
8	chr2:54272600-54286600	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr2:54272600-54286800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr2:54273000-54292400	Weak transcription	Fetal Brain Female	brain
11	chr2:54276800-54286800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr2:54277200-54290800	Weak transcription	Stomach Smooth Muscle	stomach
13	chr2:54278800-54282000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr2:54278800-54302400	Weak transcription	Left Ventricle	heart
15	chr2:54279800-54282000	ZNF genes & repeats	Primary B cells from peripheral blood	blood
16	chr2:54279800-54282000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr2:54279800-54282000	Enhancers	Brain Anterior Caudate	brain
18	chr2:54280000-54282000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
19	chr2:54280000-54282000	Enhancers	Brain Hippocampus Middle	brain
20	chr2:54280000-54292400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr2:54280200-54282000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr2:54280200-54282000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
23	chr2:54280200-54282000	Enhancers	Primary T helper cells fromperipheralblood	blood
24	chr2:54280200-54282000	Enhancers	Rectal Mucosa Donor 31	rectum
25	chr2:54280200-54286600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr2:54280400-54283400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr2:54280600-54284400	Weak transcription	Liver	Liver
28	chr2:54280800-54282000	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr2:54280800-54282800	Weak transcription	Fetal Muscle Trunk	muscle
30	chr2:54280800-54283000	Weak transcription	Rectal Smooth Muscle	rectum
31	chr2:54280800-54283200	Weak transcription	Pancreas	Pancrea
32	chr2:54280800-54285000	Weak transcription	Fetal Intestine Small	intestine
33	chr2:54280800-54286400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr2:54280800-54286800	Weak transcription	Primary hematopoietic stem cells	blood
35	chr2:54280800-54291400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr2:54280800-54310000	Weak transcription	Ovary	ovary
37	chr2:54280800-54315000	Weak transcription	Adipose Nuclei	Adipose
38	chr2:54280800-54315200	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr2:54280800-54331000	Weak transcription	Aorta	Aorta
40	chr2:54281000-54282200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
41	chr2:54281000-54291200	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr2:54281200-54282000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
43	chr2:54281200-54282000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr2:54281200-54286600	Weak transcription	Fetal Muscle Leg	muscle
45	chr2:54281200-54292400	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr2:54281400-54282400	Enhancers	Brain Substantia Nigra	brain
47	chr2:54281600-54282000	Enhancers	Brain Angular Gyrus	brain
48	chr2:54281600-54282200	Enhancers	Primary T killer memory cells from peripheral blood	blood
49	chr2:54281600-54282400	Enhancers	Stomach Mucosa	stomach
50	chr2:54281600-54286600	Weak transcription	Primary T cells from cord blood	blood

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