Variant report

Variant	rs3933010
Chromosome Location	chr1:224192088-224192089
allele	C/T
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	BATF	chr1:224191763-224192172	GM12878	blood:	n/a	n/a
2	SPI1	chr1:224191805-224192100	GM12878	blood:	n/a	chr1:224191964-224191977 chr1:224191965-224191974 chr1:224191963-224191976
3	IRF4	chr1:224191731-224192271	GM12878	blood:	n/a	n/a
4	BATF	chr1:224191763-224192234	GM12878	blood:	n/a	n/a
5	BCL11A	chr1:224191830-224192355	GM12878	blood:	n/a	chr1:224192201-224192210
6	SPI1	chr1:224191834-224192115	GM12891	blood:	n/a	chr1:224191964-224191977 chr1:224191965-224191974 chr1:224191963-224191976

Variant related genes	Relation type
ENSG00000185495	TF binding region
ENSG00000263182	TF binding region

Extended variants
information (count: 33 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10916149	0.90[AMR][1000 genomes]
rs12121620	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12562321	0.80[EUR][1000 genomes]
rs2404851	0.84[AMR][1000 genomes]
rs4653912	0.88[AMR][1000 genomes]
rs55772500	0.90[AMR][1000 genomes]
rs59220538	0.87[AMR][1000 genomes]
rs61823286	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61823340	0.87[AMR][1000 genomes]
rs61826609	0.87[AMR][1000 genomes]
rs7516230	0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:22 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757772	chr1:223935220-224363163	Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	esv2759000	chr1:223935220-224363163	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv873215	chr1:224075483-224204433	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv873216	chr1:224075483-224230307	ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv427941	chr1:224085052-224363163	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
6	nsv873218	chr1:224097155-224204433	Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Enhancers Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv873219	chr1:224097155-224216822	Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
8	nsv873220	chr1:224097155-224223659	ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
9	nsv549241	chr1:224103992-224216757	Active TSS Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
10	nsv549242	chr1:224115297-224203918	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
11	nsv549243	chr1:224115297-224216757	Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
12	nsv945316	chr1:224133366-224196526	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
13	nsv549244	chr1:224183599-224202820	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
14	nsv549245	chr1:224183599-224203686	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
15	nsv549246	chr1:224183599-224203833	ZNF genes & repeats Weak transcription Enhancers Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
16	nsv549247	chr1:224183599-224203918	ZNF genes & repeats Weak transcription Enhancers Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
17	nsv549248	chr1:224183599-224216757	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
18	nsv549249	chr1:224183599-224216822	Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
19	esv2457419	chr1:224184276-224201973	ZNF genes & repeats Strong transcription Weak transcription Enhancers Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
20	esv1845965	chr1:224184836-224194776	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
21	esv1847784	chr1:224185036-224227122	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
22	esv1795476	chr1:224186148-224226044	Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3933010	RP11-504P24.4	cis	Thyroid	GTEx
rs3933010	RP11-504P24.6	cis	Thyroid	GTEx
rs3933010	RP11-504P24.3	cis	Nerve Tibial	GTEx

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224181200-224199200	Weak transcription	Brain Substantia Nigra	brain
2	chr1:224181400-224199200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:224181600-224192400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr1:224181600-224192400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr1:224181600-224192400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr1:224181600-224193600	Weak transcription	Fetal Brain Female	brain
7	chr1:224181600-224195000	Weak transcription	HSMM	muscle
8	chr1:224181600-224195400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr1:224181600-224195800	Weak transcription	HSMMtube	muscle
10	chr1:224181600-224196400	Weak transcription	Fetal Intestine Large	intestine
11	chr1:224181600-224196400	Weak transcription	Fetal Muscle Leg	muscle
12	chr1:224181600-224196400	Weak transcription	A549	lung
13	chr1:224181600-224199000	Weak transcription	Fetal Stomach	stomach
14	chr1:224181600-224199200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr1:224181600-224199200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr1:224181600-224199200	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr1:224181600-224199200	Weak transcription	Brain Cingulate Gyrus	brain
18	chr1:224181600-224199200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr1:224181600-224199200	Weak transcription	Colon Smooth Muscle	Colon
20	chr1:224181600-224199400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr1:224181600-224199400	Weak transcription	NH-A	brain
22	chr1:224181800-224192600	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr1:224181800-224192600	Weak transcription	Liver	Liver
24	chr1:224181800-224195200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr1:224181800-224195600	Weak transcription	Fetal Intestine Small	intestine
26	chr1:224181800-224196600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr1:224181800-224197800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr1:224181800-224199200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr1:224181800-224199200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr1:224181800-224199200	Weak transcription	Primary hematopoietic stem cells	blood
31	chr1:224181800-224199200	Weak transcription	Adipose Nuclei	Adipose
32	chr1:224181800-224199200	Weak transcription	Brain Anterior Caudate	brain
33	chr1:224181800-224199200	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr1:224181800-224199200	Weak transcription	Duodenum Mucosa	Duodenum
35	chr1:224181800-224199200	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr1:224181800-224199200	Weak transcription	Fetal Kidney	kidney
37	chr1:224181800-224199200	Weak transcription	Ovary	ovary
38	chr1:224181800-224199200	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr1:224181800-224199200	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr1:224181800-224201800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr1:224182200-224192200	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr1:224182200-224192400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr1:224182200-224194800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr1:224182200-224195800	Weak transcription	Fetal Thymus	thymus
45	chr1:224182200-224198800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr1:224182200-224199000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
47	chr1:224182200-224199000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr1:224182200-224199000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr1:224182200-224199200	Weak transcription	Fetal Muscle Trunk	muscle
50	chr1:224182200-224199200	Weak transcription	Dnd41	blood

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