Variant report

Variant	rs6670477
Chromosome Location	chr1:155861810-155861811
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:155827738..155830604-chr1:155860213..155862034,2	MCF-7	breast:
2	chr1:155861450..155863047-chr1:155868429..155870558,2	K562	blood:

Variant related genes	Relation type
ENSG00000116580	Chromatin interaction
ENSG00000132718	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10796955	0.80[AMR][1000 genomes]
rs10908483	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12026057	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12037177	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12080846	0.80[AFR][1000 genomes]
rs12144175	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1889532	0.80[AMR][1000 genomes]
rs1889533	0.80[AMR][1000 genomes]
rs2016251	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2282301	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2297649	0.80[AMR][1000 genomes]
rs66466805	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs66669006	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6667652	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6696019	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72708205	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7528441	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7545308	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs867548	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs867549	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs867550	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs915181	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv33869	chr1:155223283-155917961	Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
2	esv3423892	chr1:155664084-155901487	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv916198	chr1:155804210-156403997	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	428 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6670477	RIT1	Cis_1M	lymphoblastoid	RTeQTL
rs6670477	RIT1	cis	Thyroid	GTEx
rs6670477	GON4L	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155830000-155869000	Weak transcription	Gastric	stomach
2	chr1:155830400-155865800	Weak transcription	Esophagus	oesophagus
3	chr1:155830600-155866800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr1:155831000-155862600	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr1:155831000-155862800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr1:155831000-155863000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr1:155831200-155862800	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr1:155836400-155866400	Weak transcription	Primary B cells from cord blood	blood
9	chr1:155837600-155863000	Weak transcription	Colonic Mucosa	Colon
10	chr1:155841400-155863000	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr1:155841800-155869200	Weak transcription	Right Ventricle	heart
12	chr1:155842600-155863400	Weak transcription	Right Atrium	heart
13	chr1:155844000-155862200	Weak transcription	Lung	lung
14	chr1:155844400-155874000	Weak transcription	Fetal Brain Male	brain
15	chr1:155847600-155866400	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr1:155849400-155863000	Weak transcription	Rectal Smooth Muscle	rectum
17	chr1:155849600-155862800	Weak transcription	Primary hematopoietic stem cells	blood
18	chr1:155850000-155862800	Weak transcription	Primary T helper cells PMA-I stimulated	--
19	chr1:155850400-155862400	Weak transcription	Placenta	Placenta
20	chr1:155850600-155873600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr1:155851400-155862600	Weak transcription	Adipose Nuclei	Adipose
22	chr1:155851400-155862600	Weak transcription	Stomach Smooth Muscle	stomach
23	chr1:155851400-155862800	Weak transcription	Colon Smooth Muscle	Colon
24	chr1:155851400-155863200	Weak transcription	Aorta	Aorta
25	chr1:155851400-155866000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr1:155851400-155866000	Weak transcription	Spleen	Spleen
27	chr1:155851400-155866400	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr1:155851400-155867400	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr1:155851600-155866800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr1:155851600-155870200	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr1:155852600-155862800	Weak transcription	Monocytes-CD14+_RO01746	blood
32	chr1:155852600-155863000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr1:155853000-155863400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr1:155853200-155862200	Weak transcription	Fetal Muscle Trunk	muscle
35	chr1:155853200-155863000	Weak transcription	Left Ventricle	heart
36	chr1:155853600-155862800	Weak transcription	Primary T cells fromperipheralblood	blood
37	chr1:155854200-155862400	Weak transcription	Fetal Muscle Leg	muscle
38	chr1:155854200-155868600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr1:155854400-155866200	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr1:155854400-155866400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr1:155854400-155873600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr1:155854800-155862400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr1:155854800-155862600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr1:155854800-155868800	Weak transcription	Ovary	ovary
45	chr1:155855200-155862400	Weak transcription	Brain Cingulate Gyrus	brain
46	chr1:155855200-155862600	Weak transcription	K562	blood
47	chr1:155855200-155863200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr1:155855800-155862400	Weak transcription	Fetal Intestine Small	intestine
49	chr1:155855800-155862600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr1:155855800-155862600	Weak transcription	Brain Inferior Temporal Lobe	brain

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