Variant report

Variant	rs1018490
Chromosome Location	chr22:31996625-31996626
allele	A/C
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	CTCF	chr22:31996600-31996750	K562	blood:	n/a	n/a
2	GATA3	chr22:31996578-31997086	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr22:31996113..31998454-chr22:32024863..32027924,3	MCF-7	breast:
2	chr22:31995326..31999503-chr22:32025440..32027156,3	MCF-7	breast:
3	22:31836635-31847259..22:31995181-31997770	Hela-S3	cervix:

Variant related genes	Relation type
SFI1	TF binding region
ENSG00000241878	Chromatin interaction
ENSG00000184708	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs2006771	0.80[MEX][hapmap]
rs2070274	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5749286	0.86[CHD][hapmap];0.81[JPT][hapmap]
rs5749298	0.83[CHD][hapmap];0.81[JPT][hapmap]
rs5753659	0.83[CHD][hapmap];0.81[JPT][hapmap]
rs5753669	0.85[CHD][hapmap];0.81[JPT][hapmap]
rs5753671	0.86[CHD][hapmap];0.81[JPT][hapmap]
rs5753698	0.82[CHD][hapmap];0.86[JPT][hapmap]
rs5998058	0.82[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6518752	0.84[MEX][hapmap]
rs7284622	0.81[JPT][hapmap]
rs7287937	0.80[MEX][hapmap]
rs8138525	0.82[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs8140312	0.84[MKK][hapmap]
rs9606848	0.86[CHD][hapmap];0.81[JPT][hapmap]
rs9609296	0.83[CHD][hapmap];0.81[JPT][hapmap]
rs9609297	0.85[CHD][hapmap];0.81[JPT][hapmap]
rs9609304	0.83[CHD][hapmap];0.81[JPT][hapmap]
rs9609329	0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv914980	chr22:31966274-32024980	Weak transcription Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv517534	chr22:31977594-32024980	Flanking Active TSS Genic enhancers Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1018490	SFI1	cis	Thyroid	GTEx
rs1018490	PATZ1	cis	parietal	SCAN
rs1018490	RFPL2	cis	cerebellum	SCAN
rs1018490	RNF185	cis	cerebellum	SCAN

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:31935800-32013200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr22:31947800-32009600	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr22:31949400-32014400	Weak transcription	Hela-S3	cervix
4	chr22:31957400-32016400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr22:31968800-32003800	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr22:31974400-31998200	Weak transcription	Small Intestine	intestine
7	chr22:31974800-31998200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr22:31975000-32003800	Weak transcription	Aorta	Aorta
9	chr22:31976200-32014800	Weak transcription	A549	lung
10	chr22:31976400-32014800	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr22:31976400-32019200	Weak transcription	Fetal Brain Male	brain
12	chr22:31982000-31998000	Weak transcription	Brain Angular Gyrus	brain
13	chr22:31982400-31998200	Weak transcription	Gastric	stomach
14	chr22:31982600-31997400	Weak transcription	Brain Hippocampus Middle	brain
15	chr22:31982600-31998000	Weak transcription	NHEK	skin
16	chr22:31982600-31998400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr22:31982600-32006400	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr22:31982800-31997600	Weak transcription	Colon Smooth Muscle	Colon
19	chr22:31982800-31998200	Weak transcription	NHLF	lung
20	chr22:31983000-31998600	Weak transcription	Colonic Mucosa	Colon
21	chr22:31983600-31998000	Weak transcription	Spleen	Spleen
22	chr22:31984400-31996800	Weak transcription	GM12878-XiMat	blood
23	chr22:31984400-31998000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr22:31984400-31998000	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr22:31984400-31998200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr22:31984400-31998400	Weak transcription	Primary B cells from cord blood	blood
27	chr22:31984400-31998400	Weak transcription	Adipose Nuclei	Adipose
28	chr22:31984400-31998400	Weak transcription	Fetal Lung	lung
29	chr22:31984400-31999000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr22:31984600-31997600	Weak transcription	Fetal Muscle Leg	muscle
31	chr22:31984600-31997800	Weak transcription	Stomach Smooth Muscle	stomach
32	chr22:31984600-31998000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr22:31984600-31998200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr22:31984600-31998200	Weak transcription	Ovary	ovary
35	chr22:31985200-31998200	Weak transcription	Fetal Brain Female	brain
36	chr22:31985600-31997800	Weak transcription	Primary monocytes fromperipheralblood	blood
37	chr22:31985600-31998000	Weak transcription	Osteobl	bone
38	chr22:31985600-31998400	Weak transcription	Brain Anterior Caudate	brain
39	chr22:31985600-32014000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr22:31985800-31996800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr22:31985800-31997600	Weak transcription	Primary neutrophils fromperipheralblood	blood
42	chr22:31985800-31997600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr22:31985800-31997600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
44	chr22:31985800-31997600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr22:31985800-31997600	Weak transcription	Duodenum Mucosa	Duodenum
46	chr22:31985800-31997800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr22:31985800-31997800	Weak transcription	Cortex derived primary cultured neurospheres	brain
48	chr22:31985800-31997800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr22:31985800-31997800	Weak transcription	Brain Germinal Matrix	brain
50	chr22:31985800-31997800	Weak transcription	Sigmoid Colon	Sigmoid Colon

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