Variant report

Variant	rs4074668
Chromosome Location	chr1:228072809-228072810
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:228072172..228075601-chr1:228081221..228085258,4	K562	blood:
2	chr1:228064722..228067770-chr1:228071905..228075743,3	K562	blood:
3	chr1:228070687..228073614-chr1:228077834..228079933,2	MCF-7	breast:
4	chr1:228072191..228073932-chr1:228079924..228082408,2	K562	blood:
5	chr1:228067787..228070478-chr1:228072728..228075273,4	K562	blood:
6	chr1:228070680..228073922-chr1:228077566..228080384,3	MCF-7	breast:

Extended variants
information (count: 17 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs2313202	0.83[ASN][1000 genomes]
rs55856451	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6686787	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73104847	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73104870	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs74140397	1.00[EUR][1000 genomes];1.00[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	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
2	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
3	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
4	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
5	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
6	nsv1005852	chr1:227957099-228148363	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
7	nsv535319	chr1:227957099-228148363	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
8	nsv516409	chr1:228035131-228296745	Enhancers Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
9	nsv523935	chr1:228038124-228681749	Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	137 gene(s)	inside rSNPs	diseases
10	nsv873250	chr1:228051234-228121548	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv873251	chr1:228051234-228160911	Enhancers Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4074668	MIXL1	cis	cerebellum	SCAN
rs4074668	C1orf96	cis	parietal	SCAN
rs4074668	PSEN2	cis	lymphoblastoid	seeQTL
rs4074668	LIN9	cis	cerebellum	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228068400-228073200	Weak transcription	Gastric	stomach
2	chr1:228070600-228073200	Enhancers	Primary T cells fromperipheralblood	blood
3	chr1:228070600-228073200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr1:228070800-228073000	Enhancers	Primary T helper cells PMA-I stimulated	--
5	chr1:228070800-228073000	Enhancers	Primary T helper cells fromperipheralblood	blood
6	chr1:228070800-228074200	Enhancers	Esophagus	oesophagus
7	chr1:228071000-228073000	Enhancers	Primary T helper naive cells from peripheral blood	blood
8	chr1:228071000-228074000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
9	chr1:228071200-228073000	Weak transcription	NHEK	skin
10	chr1:228071400-228073000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
11	chr1:228071400-228073000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr1:228071400-228073400	Weak transcription	Pancreas	Pancrea
13	chr1:228071600-228073000	Enhancers	Primary T cells from cord blood	blood
14	chr1:228071600-228073200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
15	chr1:228071800-228073000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr1:228071800-228073200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
17	chr1:228071800-228074600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
18	chr1:228072000-228073000	Enhancers	Primary T killer memory cells from peripheral blood	blood
19	chr1:228072200-228073000	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr1:228072200-228073200	Enhancers	Stomach Smooth Muscle	stomach
21	chr1:228072200-228074200	Enhancers	Fetal Stomach	stomach
22	chr1:228072400-228074200	Enhancers	Thymus	Thymus
23	chr1:228072400-228074800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
24	chr1:228072400-228075200	Enhancers	Breast Myoepithelial Primary Cells	Breast
25	chr1:228072600-228073000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
26	chr1:228072600-228073000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr1:228072600-228073000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr1:228072600-228074400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr1:228072600-228074400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr1:228072600-228074400	Enhancers	Fetal Muscle Leg	muscle
31	chr1:228072600-228075600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
32	chr1:228072800-228073000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
33	chr1:228072800-228073200	Enhancers	HMEC	breast
34	chr1:228072800-228074600	Enhancers	Primary B cells from cord blood	blood

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