Variant report

Variant	rs41270167
Chromosome Location	chr1:227923992-227923993
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	E2F6	chr1:227923838-227924003	K562	blood:	n/a	n/a
2	POLR2A	chr1:227922205-227924256	PBDE	blood:	n/a	n/a
3	MAZ	chr1:227922175-227924196	IMR90	lung:	n/a	chr1:227922598-227922607
4	POLR2A	chr1:227921936-227924227	MCF10A-Er-Src	breast:	n/a	n/a
5	FOXA1	chr1:227923925-227924179	T-47D	breast:	n/a	n/a
6	ZNF263	chr1:227922204-227924083	HEK293-T-REx	kidney:	n/a	chr1:227923299-227923308
7	POLR2A	chr1:227922147-227924196	K562	blood:	n/a	n/a
8	POLR2A	chr1:227923850-227924003	HepG2	liver:	n/a	n/a
9	POLR2A	chr1:227923878-227924081	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr1:227922079-227924238	MCF10A-Er-Src	breast:	n/a	n/a
11	POLR2A	chr1:227922288-227924128	H1-hESC	embryonic stem cell:	n/a	n/a
12	FOXA2	chr1:227923870-227924132	A549	lung:	n/a	n/a
13	FOXA1	chr1:227923841-227924164	T-47D	breast:	n/a	n/a
14	JUN	chr1:227921816-227924147	K562	blood:	n/a	n/a
15	SMARCB1	chr1:227922280-227924057	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:227922958..227924817-chr1:228133058..228135872,2	MCF-7	breast:
2	chr1:227918805..227924684-chr1:227929963..227939883,12	K562	blood:
3	chr1:227923000..227925656-chr1:228268639..228271303,2	MCF-7	breast:
4	chr1:227921956..227924183-chr1:227932541..227935696,3	MCF-7	breast:

Variant related genes	Relation type
JMJD4	TF binding region
ENSG00000230005	Chromatin interaction
ENSG00000143740	Chromatin interaction
ENSG00000143761	Chromatin interaction
ENSG00000143816	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1570429	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16848110	0.97[EUR][1000 genomes]
rs17851681	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2029836	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2273936	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3806264	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41270161	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41305134	0.81[EUR][1000 genomes]
rs4837	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58565844	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs748405	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7543525	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	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
3	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
4	esv32853	chr1:227880116-228806209	Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
5	nsv427952	chr1:227881664-228308629	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
6	nsv826908	chr1:227895386-228691100	Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
7	nsv515496	chr1:227912474-227967938	Active TSS Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
8	nsv873249	chr1:227920061-228121548	Weak transcription Bivalent Enhancer Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
9	esv3375515	chr1:227921854-227924702	Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs41270167	ZNF678	cis	Muscle Skeletal	GTEx
rs41270167	C1orf142	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227921600-227924200	Active TSS	iPS-18 Cell Line	embryonic stem cell
2	chr1:227921600-227924200	Active TSS	iPS-20b Cell Line	embryonic stem cell
3	chr1:227921800-227924200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr1:227921800-227924200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr1:227921800-227924200	Active TSS	HUES6 Cell Line	embryonic stem cell
6	chr1:227921800-227924200	Active TSS	HUES64 Cell Line	embryonic stem cell
7	chr1:227921800-227924200	Active TSS	A549	lung
8	chr1:227922000-227924000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr1:227922000-227924000	Active TSS	H9 Cell Line	embryonic stem cell
10	chr1:227922000-227924000	Active TSS	iPS-15b Cell Line	embryonic stem cell
11	chr1:227922000-227924000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
12	chr1:227922000-227924000	Flanking Active TSS	Primary hematopoietic stem cells	blood
13	chr1:227922000-227924000	Active TSS	Fetal Kidney	kidney
14	chr1:227922000-227924000	Active TSS	Pancreatic Islets	Pancreatic Islet
15	chr1:227922000-227924200	Active TSS	ES-I3 Cell Line	embryonic stem cell
16	chr1:227922000-227924200	Active TSS	HUES48 Cell Line	embryonic stem cell
17	chr1:227922200-227924000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr1:227922200-227924000	Active TSS	Muscle Satellite Cultured Cells	--
19	chr1:227922200-227924000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
20	chr1:227922200-227924200	Active TSS	Fetal Intestine Large	intestine
21	chr1:227922400-227924000	Active TSS	HSMM	muscle
22	chr1:227922600-227924000	Active TSS	HepG2	liver
23	chr1:227923400-227924000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
24	chr1:227923400-227924000	Flanking Active TSS	Primary B cells from peripheral blood	blood
25	chr1:227923400-227924000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
26	chr1:227923400-227924000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
27	chr1:227923400-227924000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
28	chr1:227923400-227924000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
29	chr1:227923400-227924000	Flanking Active TSS	Liver	Liver
30	chr1:227923400-227924000	Flanking Active TSS	Esophagus	oesophagus
31	chr1:227923400-227924000	Flanking Active TSS	Fetal Muscle Leg	muscle
32	chr1:227923400-227924000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
33	chr1:227923400-227924200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr1:227923400-227924200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr1:227923400-227924200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
36	chr1:227923400-227924200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
37	chr1:227923400-227924200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr1:227923400-227924200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr1:227923400-227924200	Flanking Active TSS	Adipose Nuclei	Adipose
40	chr1:227923400-227924200	Flanking Active TSS	Brain Germinal Matrix	brain
41	chr1:227923400-227924200	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
42	chr1:227923400-227924200	Flanking Active TSS	Colonic Mucosa	Colon
43	chr1:227923400-227924200	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
44	chr1:227923400-227924200	Flanking Active TSS	Fetal Brain Male	brain
45	chr1:227923400-227924200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
46	chr1:227923400-227924200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
47	chr1:227923400-227925000	Flanking Active TSS	Stomach Smooth Muscle	stomach
48	chr1:227923600-227924000	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr1:227923600-227924000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr1:227923600-227924000	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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