Variant report

Variant	rs10916174
Chromosome Location	chr1:227804041-227804042
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:227803218..227804951-chr1:227810975..227813465,2	MCF-7	breast:
2	chr1:227749534..227751612-chr1:227801658..227804167,2	K562	blood:
3	chr1:227797816..227799614-chr1:227803015..227804639,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000181450	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10799428	0.80[EUR][1000 genomes]
rs10916167	0.81[EUR][1000 genomes]
rs12129894	0.81[EUR][1000 genomes]
rs12140813	0.81[EUR][1000 genomes]
rs12140848	0.81[EUR][1000 genomes]
rs59885016	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7540754	0.96[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7549475	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534002	chr1:227315186-228047108	Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
2	nsv873246	chr1:227694948-227884465	Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv1007479	chr1:227695868-227984466	Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription 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	33 gene(s)	inside rSNPs	diseases
4	esv3327012	chr1:227741102-227890968	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv1010605	chr1:227770415-228332690	Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
6	nsv945673	chr1:227799341-227819395	ZNF genes & repeats Weak transcription Strong transcription Enhancers Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10916174	JMJD4	cis	multi-tissue	Pritchard
rs10916174	ZNF678	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227770000-227853800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr1:227774800-227805000	Weak transcription	Brain Hippocampus Middle	brain
3	chr1:227790400-227834800	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr1:227794400-227804400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr1:227794600-227808600	Weak transcription	Left Ventricle	heart
6	chr1:227795200-227807000	Weak transcription	Fetal Heart	heart
7	chr1:227796200-227807200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr1:227796800-227806000	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr1:227797600-227804800	ZNF genes & repeats	Fetal Stomach	stomach
10	chr1:227797800-227804800	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr1:227797800-227805800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
12	chr1:227797800-227806400	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
13	chr1:227797800-227807200	ZNF genes & repeats	Fetal Brain Female	brain
14	chr1:227798000-227804200	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr1:227798000-227806400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
16	chr1:227798200-227806800	ZNF genes & repeats	Brain Germinal Matrix	brain
17	chr1:227798200-227806800	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
18	chr1:227798200-227806800	ZNF genes & repeats	Fetal Muscle Leg	muscle
19	chr1:227798200-227808000	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr1:227799400-227805000	ZNF genes & repeats	Lung	lung
21	chr1:227800200-227805000	Weak transcription	Brain Substantia Nigra	brain
22	chr1:227800200-227805600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr1:227800200-227820600	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr1:227800400-227804600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr1:227800400-227805000	Weak transcription	Adipose Nuclei	Adipose
26	chr1:227800400-227807000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr1:227800400-227814200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr1:227800600-227804800	Weak transcription	Gastric	stomach
29	chr1:227800800-227805000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr1:227801000-227807200	ZNF genes & repeats	Primary T cells from cord blood	blood
31	chr1:227801200-227821800	Weak transcription	Stomach Smooth Muscle	stomach
32	chr1:227801400-227804400	Weak transcription	Brain Angular Gyrus	brain
33	chr1:227801600-227805200	ZNF genes & repeats	Liver	Liver
34	chr1:227801600-227805200	Weak transcription	Fetal Intestine Large	intestine
35	chr1:227801800-227804200	Weak transcription	Primary B cells from peripheral blood	blood
36	chr1:227802200-227806200	ZNF genes & repeats	Dnd41	blood
37	chr1:227802600-227804200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr1:227802600-227806200	ZNF genes & repeats	Primary B cells from cord blood	blood
39	chr1:227802600-227808200	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
40	chr1:227803000-227805800	ZNF genes & repeats	Fetal Muscle Trunk	muscle
41	chr1:227803000-227806000	ZNF genes & repeats	Aorta	Aorta
42	chr1:227803200-227805400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr1:227803200-227806000	ZNF genes & repeats	A549	lung
44	chr1:227803400-227804600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr1:227803400-227806000	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
46	chr1:227803400-227806200	ZNF genes & repeats	Fetal Intestine Small	intestine
47	chr1:227803600-227804600	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr1:227803600-227805400	Strong transcription	Ovary	ovary
49	chr1:227803800-227804600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr1:227803800-227804600	Weak transcription	Pancreas	Pancrea

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