Variant report

Variant	rs1322775
Chromosome Location	chr1:173855298-173855299
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:173853137..173856860-chr1:173858771..173862944,6	K562	blood:
2	chr1:173828135..173830893-chr1:173854579..173857617,3	MCF-7	breast:
3	chr1:173844210..173845835-chr1:173854372..173856264,2	K562	blood:
4	chr1:173854070..173860394-chr1:173860539..173867294,11	MCF-7	breast:
5	chr1:173842881..173845710-chr1:173854372..173856048,2	K562	blood:
6	chr1:173853219..173856006-chr1:173864250..173866339,2	K562	blood:
7	chr1:173846519..173848923-chr1:173855106..173856720,2	K562	blood:
8	chr1:173836574..173839930-chr1:173853408..173856116,3	K562	blood:
9	chr1:173855077..173857182-chr1:173858771..173861573,3	K562	blood:
10	chr1:173831191..173840458-chr1:173852193..173864862,18	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000208317	Chromatin interaction
ENSG00000185278	Chromatin interaction
ENSG00000270084	Chromatin interaction
ENSG00000234741	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10798295	0.82[CHB][hapmap];0.91[JPT][hapmap]
rs10798301	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs10798302	0.87[CHB][hapmap]
rs12066153	0.87[CHB][hapmap]
rs12071594	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12071663	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12078824	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1322770	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1322777	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1322780	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1799876	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1884994	0.83[CHB][hapmap]
rs1951627	0.87[CHB][hapmap];1.00[YRI][hapmap]
rs2065171	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4652229	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4971204	0.88[YRI][hapmap]
rs5877	0.96[CEU][hapmap];0.85[CHB][hapmap];0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs5878	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6663875	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6665484	0.87[CHB][hapmap]
rs6677660	0.87[CHB][hapmap]
rs6686083	0.87[CHB][hapmap]
rs6689285	0.87[CHB][hapmap]
rs6696163	0.87[CHB][hapmap]
rs714624	0.87[CHB][hapmap]
rs7349095	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7413166	0.86[CHB][hapmap]
rs7544605	0.85[AMR][1000 genomes]
rs7552939	0.82[CHB][hapmap];0.91[JPT][hapmap];0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9286895	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs941989	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9425430	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9425435	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9425755	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9425765	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9425766	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9661233	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012384	chr1:173614816-173974426	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	294 gene(s)	inside rSNPs	diseases
2	nsv831926	chr1:173702403-173894667	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	291 gene(s)	inside rSNPs	diseases
3	esv2757761	chr1:173810642-173955943	Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	264 gene(s)	inside rSNPs	diseases
4	esv2758978	chr1:173810642-173955943	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	264 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1322775		cis	Lymphoblastoid	GTEx

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:173838200-173866000	Weak transcription	Small Intestine	intestine
2	chr1:173838400-173860200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr1:173838800-173855800	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr1:173839000-173862800	Weak transcription	HMEC	breast
5	chr1:173840200-173856800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:173841000-173864400	Weak transcription	Fetal Heart	heart
7	chr1:173841000-173868600	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr1:173842800-173859200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr1:173846200-173856000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr1:173847800-173855800	Weak transcription	Fetal Brain Male	brain
11	chr1:173849200-173856000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr1:173853200-173855800	Strong transcription	Fetal Intestine Small	intestine
13	chr1:173853200-173856000	Strong transcription	Fetal Stomach	stomach
14	chr1:173853200-173858000	Strong transcription	Fetal Muscle Leg	muscle
15	chr1:173853400-173856400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr1:173853400-173857800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr1:173853400-173865200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr1:173853800-173855800	Strong transcription	Primary T cells from cord blood	blood
19	chr1:173853800-173858600	Strong transcription	Placenta	Placenta
20	chr1:173854000-173855400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr1:173854000-173855600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr1:173854000-173857400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr1:173854000-173858800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr1:173854000-173858800	Strong transcription	Primary monocytes fromperipheralblood	blood
25	chr1:173854000-173859400	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr1:173854200-173855400	Strong transcription	Primary T helper naive cells from peripheral blood	blood
27	chr1:173854200-173855400	Strong transcription	Colonic Mucosa	Colon
28	chr1:173854200-173855600	Strong transcription	Primary T helper cells fromperipheralblood	blood
29	chr1:173854200-173855800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr1:173854200-173856000	Strong transcription	Esophagus	oesophagus
31	chr1:173854200-173856000	Strong transcription	Gastric	stomach
32	chr1:173854200-173856200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr1:173854200-173856200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr1:173854200-173856200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr1:173854200-173856200	Strong transcription	Lung	lung
36	chr1:173854200-173856200	Strong transcription	Dnd41	blood
37	chr1:173854200-173856200	Strong transcription	NHLF	lung
38	chr1:173854200-173856800	Strong transcription	Cortex derived primary cultured neurospheres	brain
39	chr1:173854200-173857000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr1:173854200-173857000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr1:173854200-173857200	Strong transcription	Brain Anterior Caudate	brain
42	chr1:173854200-173857600	Strong transcription	Primary B cells from peripheral blood	blood
43	chr1:173854200-173858200	Strong transcription	Left Ventricle	heart
44	chr1:173854200-173858800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr1:173854400-173856400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr1:173854600-173855400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
47	chr1:173854600-173855600	Strong transcription	Pancreas	Pancrea
48	chr1:173854600-173856000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr1:173854600-173856000	Strong transcription	Hela-S3	cervix
50	chr1:173854600-173856200	Strong transcription	Muscle Satellite Cultured Cells	--

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