Variant report

Variant	rs7365254
Chromosome Location	chr1:246888826-246888827
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:246858802..246860634-chr1:246887473..246889819,2	MCF-7	breast:
2	chr1:246853163..246855096-chr1:246886538..246888986,3	MCF-7	breast:
3	chr1:246862215..246864763-chr1:246888186..246891481,3	K562	blood:
4	chr1:246853196..246855742-chr1:246886661..246889205,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000235021	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1127098	1.00[CEU][hapmap];0.86[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1127149	1.00[CEU][hapmap];0.82[JPT][hapmap];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12034911	0.81[EUR][1000 genomes]
rs12121187	0.90[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12121214	0.82[AMR][1000 genomes]
rs12128579	0.90[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12129386	0.86[JPT][hapmap];0.96[ASN][1000 genomes]
rs12129828	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12402095	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12403128	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12407065	0.85[EUR][1000 genomes]
rs12409066	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12410595	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12735300	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3087781	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34048530	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs34677128	1.00[ASN][1000 genomes]
rs35021082	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35570407	1.00[ASN][1000 genomes]
rs35736382	1.00[ASN][1000 genomes]
rs3795469	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4078128	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs41310575	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4926440	1.00[CEU][hapmap];0.82[JPT][hapmap];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4926442	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4926443	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4926444	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4926447	0.95[AMR][1000 genomes]
rs4926449	1.00[CEU][hapmap];0.86[JPT][hapmap];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4926450	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4926456	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61684731	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs61852479	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs61852481	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs61852482	0.96[ASN][1000 genomes]
rs6426329	1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6668806	1.00[CEU][hapmap];0.85[JPT][hapmap];0.81[EUR][1000 genomes]
rs6682900	0.85[AMR][1000 genomes]
rs6689579	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6697433	1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6697526	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6699332	1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6701991	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7366187	0.82[JPT][hapmap];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7410830	0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs74152239	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7513496	1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7526237	0.82[JPT][hapmap];0.92[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7528002	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7550482	0.86[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7551836	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs9659021	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002805	chr1:246608164-246890518	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
2	nsv535413	chr1:246608164-246890518	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	nsv949571	chr1:246688635-247240863	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv873421	chr1:246818634-247044692	Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	esv2762192	chr1:246823857-247069232	Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
6	nsv1006271	chr1:246832606-247276182	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
7	nsv535416	chr1:246832606-247276182	Strong transcription ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
8	nsv430413	chr1:246845971-246975015	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
9	nsv873422	chr1:246854862-247002638	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
10	nsv1011346	chr1:246868799-247133898	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
11	nsv870294	chr1:246877043-246927940	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7365254	SCCPDH	cis	multi-tissue	Pritchard
rs7365254	SCCPDH	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:246886600-246889000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr1:246886800-246889000	Active TSS	Duodenum Mucosa	Duodenum
3	chr1:246886800-246889000	Active TSS	Rectal Smooth Muscle	rectum
4	chr1:246886800-246889200	Active TSS	NHDF-Ad	bronchial
5	chr1:246887000-246889000	Active TSS	Colonic Mucosa	Colon
6	chr1:246887000-246889000	Active TSS	Fetal Brain Male	brain
7	chr1:246887000-246889200	Active TSS	Pancreatic Islets	Pancreatic Islet
8	chr1:246887800-246889000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr1:246888000-246889000	Flanking Active TSS	Primary hematopoietic stem cells	blood
10	chr1:246888000-246889000	Active TSS	Right Atrium	heart
11	chr1:246888000-246889000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
12	chr1:246888000-246889200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
13	chr1:246888000-246889800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr1:246888200-246889000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr1:246888200-246889000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
16	chr1:246888200-246889000	Flanking Active TSS	Brain Hippocampus Middle	brain
17	chr1:246888200-246889000	Flanking Active TSS	NH-A	brain
18	chr1:246888200-246889000	Flanking Active TSS	Osteobl	bone
19	chr1:246888200-246889200	Flanking Active TSS	Adipose Nuclei	Adipose
20	chr1:246888200-246889200	Flanking Active TSS	Dnd41	blood
21	chr1:246888200-246889200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
22	chr1:246888400-246889000	Flanking Active TSS	Brain Anterior Caudate	brain
23	chr1:246888400-246889000	Flanking Active TSS	Fetal Heart	heart
24	chr1:246888400-246889000	Flanking Active TSS	Fetal Lung	lung
25	chr1:246888400-246889000	Enhancers	Placenta Amnion	Placenta Amnion
26	chr1:246888400-246889000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
27	chr1:246888400-246889000	Flanking Active TSS	A549	lung
28	chr1:246888400-246889200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
29	chr1:246888400-246889200	Flanking Active TSS	Stomach Smooth Muscle	stomach
30	chr1:246888400-246889400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr1:246888400-246889800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr1:246888400-246890600	Enhancers	Primary neutrophils fromperipheralblood	blood
33	chr1:246888400-246890800	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr1:246888400-246891000	Weak transcription	Aorta	Aorta
35	chr1:246888400-246891600	Weak transcription	Esophagus	oesophagus
36	chr1:246888400-246893400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr1:246888400-246896000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr1:246888400-246900000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
39	chr1:246888400-246902000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr1:246888400-246903800	Weak transcription	Primary B cells from peripheral blood	blood
41	chr1:246888400-246946400	Weak transcription	Small Intestine	intestine
42	chr1:246888600-246889000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr1:246888600-246889000	Flanking Active TSS	Brain Angular Gyrus	brain
44	chr1:246888600-246889000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
45	chr1:246888600-246889000	Flanking Active TSS	Colon Smooth Muscle	Colon
46	chr1:246888600-246889000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
47	chr1:246888600-246889000	Flanking Active TSS	Fetal Intestine Large	intestine
48	chr1:246888600-246889000	Flanking Active TSS	Fetal Intestine Small	intestine
49	chr1:246888600-246889000	Flanking Active TSS	Fetal Kidney	kidney
50	chr1:246888600-246889000	Flanking Active TSS	Fetal Muscle Leg	muscle

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