Variant report

Variant	rs1877908
Chromosome Location	chr2:54368014-54368015
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:54342420..54344345-chr2:54367915..54370149,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000170634	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10183655	0.81[CHD][hapmap]
rs1075264	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11890838	0.86[CHD][hapmap]
rs17039547	0.91[CHB][hapmap];0.90[CHD][hapmap];0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs17045474	0.83[JPT][hapmap]
rs17045488	0.82[CHB][hapmap]
rs1877907	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2287639	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2287643	0.86[CHB][hapmap];0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs34498089	0.88[CHD][hapmap]
rs3731967	0.83[CHD][hapmap]
rs4671861	0.88[ASN][1000 genomes]
rs62137980	0.86[ASN][1000 genomes]
rs6545386	0.85[ASN][1000 genomes]
rs6706363	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6713088	0.81[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6721970	0.82[CHB][hapmap];0.82[ASN][1000 genomes]
rs6746965	0.84[JPT][hapmap]
rs6751105	0.89[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];0.89[JPT][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7559380	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7565453	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 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
9	esv1851003	chr2:54324701-54372931	Genic enhancers Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
10	nsv1007731	chr2:54331179-54452329	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
11	nsv535723	chr2:54331179-54452329	Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
12	nsv1006984	chr2:54343466-54384094	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
13	nsv874148	chr2:54344325-54432222	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
14	nsv1000652	chr2:54345892-54469703	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
15	nsv1003889	chr2:54347750-54424601	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
16	nsv582011	chr2:54348704-54384927	Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
17	nsv1011433	chr2:54351145-54424601	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
18	nsv1012230	chr2:54351988-54422959	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
19	nsv874149	chr2:54358517-54432222	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1877908	PSME4	cis	lymphoblastoid	seeQTL
rs1877908	TSPYL6	cis	cerebellum	SCAN

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54343400-54388600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr2:54350600-54382600	Weak transcription	Aorta	Aorta
3	chr2:54352200-54411400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr2:54359800-54370800	Weak transcription	Small Intestine	intestine
5	chr2:54360600-54382400	Weak transcription	Primary T helper cells PMA-I stimulated	--
6	chr2:54361200-54374200	Weak transcription	HSMMtube	muscle
7	chr2:54361400-54389800	Weak transcription	Lung	lung
8	chr2:54362000-54386800	Weak transcription	Brain Cingulate Gyrus	brain
9	chr2:54362000-54416400	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr2:54362200-54391400	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr2:54362200-54411200	Weak transcription	Stomach Smooth Muscle	stomach
12	chr2:54362400-54379400	Weak transcription	Brain Anterior Caudate	brain
13	chr2:54362400-54379400	Weak transcription	Ovary	ovary
14	chr2:54362400-54382400	Weak transcription	Brain Hippocampus Middle	brain
15	chr2:54362400-54382400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr2:54362400-54382600	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr2:54362400-54386800	Weak transcription	Brain Substantia Nigra	brain
18	chr2:54362600-54370400	Weak transcription	Liver	Liver
19	chr2:54362600-54382600	Weak transcription	Right Ventricle	heart
20	chr2:54362800-54387000	Weak transcription	Brain Angular Gyrus	brain
21	chr2:54363000-54377000	Weak transcription	Fetal Lung	lung
22	chr2:54363200-54375800	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr2:54363800-54377200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr2:54363800-54377200	Weak transcription	Fetal Muscle Leg	muscle
25	chr2:54364000-54382600	Weak transcription	HSMM	muscle
26	chr2:54364800-54375400	Weak transcription	Pancreas	Pancrea
27	chr2:54364800-54377000	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr2:54364800-54380400	Weak transcription	Primary hematopoietic stem cells	blood
29	chr2:54365800-54369200	Strong transcription	Skeletal Muscle Female	skeletal muscle
30	chr2:54366000-54368600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
31	chr2:54366400-54373200	Weak transcription	Primary T cells from cord blood	blood
32	chr2:54366400-54380000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr2:54366400-54380800	Weak transcription	Fetal Intestine Small	intestine
34	chr2:54366400-54389200	Weak transcription	Fetal Stomach	stomach
35	chr2:54366400-54391200	Weak transcription	Spleen	Spleen
36	chr2:54366400-54397200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr2:54366600-54371000	Weak transcription	Primary T helper cells fromperipheralblood	blood
38	chr2:54366600-54379400	Weak transcription	Primary B cells from peripheral blood	blood
39	chr2:54366600-54382400	Weak transcription	Left Ventricle	heart
40	chr2:54366600-54409600	Weak transcription	Psoas Muscle	Psoas
41	chr2:54366800-54374400	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr2:54366800-54376400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr2:54367400-54416600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr2:54367600-54370600	Weak transcription	HepG2	liver
45	chr2:54367600-54382600	Weak transcription	Primary B cells from cord blood	blood
46	chr2:54368000-54377000	Weak transcription	Adipose Nuclei	Adipose
47	chr2:54368000-54383800	Weak transcription	Gastric	stomach

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