Variant report

Variant	rs2364400
Chromosome Location	chr1:155997173-155997174
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:155987340..155997180-chr1:156020881..156026682,16	K562	blood:
2	chr1:155995748..155997577-chr1:156018249..156020875,2	K562	blood:
3	chr1:155989348..155992216-chr1:155996546..156001769,5	MCF-7	breast:
4	chr1:155988906..155990877-chr1:155996101..155997789,2	MCF-7	breast:
5	chr1:155994840..155997180-chr1:156020881..156023261,2	K562	blood:
6	chr1:155995911..155999462-chr1:156000578..156005266,5	K562	blood:
7	chr1:155988173..156003032-chr1:156020965..156026206,23	MCF-7	breast:

Variant related genes	Relation type
ENSG00000160803	Chromatin interaction
ENSG00000163479	Chromatin interaction
ENSG00000116586	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10908486	1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11577179	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11582305	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12032631	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12043212	0.92[CEU][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12128541	1.00[CEU][hapmap];0.90[CHB][hapmap];0.92[JPT][hapmap];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1475766	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17381047	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17385065	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1966243	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2095402	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2297792	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2364401	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2886070	1.00[CEU][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34126883	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34444588	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34995046	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4330912	0.81[AMR][1000 genomes]
rs4661079	1.00[CEU][hapmap];0.90[CHB][hapmap];0.92[JPT][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6668204	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7517202	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2364400	RIT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155990800-156006000	Weak transcription	Spleen	Spleen
2	chr1:155990800-156006800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr1:155991000-156002600	Weak transcription	NHLF	lung
4	chr1:155991000-156005800	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr1:155991000-156011600	Weak transcription	Colonic Mucosa	Colon
6	chr1:155991200-156002800	Weak transcription	NH-A	brain
7	chr1:155991200-156005600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr1:155991200-156005600	Weak transcription	Brain Angular Gyrus	brain
9	chr1:155991200-156005800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr1:155991200-156005800	Weak transcription	Liver	Liver
11	chr1:155991200-156005800	Weak transcription	Brain Anterior Caudate	brain
12	chr1:155991200-156005800	Weak transcription	Fetal Thymus	thymus
13	chr1:155991200-156006000	Weak transcription	Primary T helper cells PMA-I stimulated	--
14	chr1:155991200-156006000	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr1:155991200-156006600	Weak transcription	Brain Hippocampus Middle	brain
16	chr1:155991200-156006600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr1:155991200-156010800	Weak transcription	Fetal Heart	heart
18	chr1:155991200-156020000	Weak transcription	GM12878-XiMat	blood
19	chr1:155992200-156005800	Weak transcription	Dnd41	blood
20	chr1:155994800-156005800	Weak transcription	Brain Germinal Matrix	brain
21	chr1:155995800-156004400	Weak transcription	Fetal Muscle Leg	muscle
22	chr1:155996000-155997400	Weak transcription	Duodenum Mucosa	Duodenum
23	chr1:155996000-156002600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr1:155996000-156005600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr1:155996000-156005600	Weak transcription	Fetal Muscle Trunk	muscle
26	chr1:155996000-156005800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr1:155996000-156005800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr1:155996000-156005800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr1:155996000-156010400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr1:155996200-155999400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr1:155996200-155999400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr1:155996200-155999600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr1:155996200-155999600	Weak transcription	HepG2	liver
34	chr1:155996200-156000000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr1:155996200-156005400	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr1:155996200-156005400	Weak transcription	Placenta	Placenta
37	chr1:155996200-156005600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr1:155996200-156005800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr1:155996200-156005800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr1:155996200-156005800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr1:155996200-156005800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr1:155996200-156005800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr1:155996200-156005800	Weak transcription	Adipose Nuclei	Adipose
44	chr1:155996200-156005800	Weak transcription	Fetal Intestine Large	intestine
45	chr1:155996200-156005800	Weak transcription	Fetal Intestine Small	intestine
46	chr1:155996200-156005800	Weak transcription	Lung	lung
47	chr1:155996200-156005800	Weak transcription	Pancreas	Pancrea
48	chr1:155996200-156005800	Weak transcription	A549	lung
49	chr1:155996200-156005800	Weak transcription	K562	blood
50	chr1:155996200-156006000	Weak transcription	HUES48 Cell Line	embryonic stem cell

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