Variant report

Variant	rs1044478
Chromosome Location	chr1:160966963-160966964
allele	A/G
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:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:160965718..160968387-chr1:160991950..160993671,3	MCF-7	breast:
2	chr1:160965107..160967123-chr1:161018782..161021042,2	MCF-7	breast:
3	chr1:160965945..160967708-chr1:160990265..160992249,2	K562	blood:
4	chr1:160965921..160968886-chr1:161007500..161010236,2	K562	blood:
5	chr1:160965718..160969126-chr1:160976993..160979194,4	K562	blood:
6	chr1:160959131..160961760-chr1:160965672..160967249,2	K562	blood:
7	chr1:160966862..160967727-chr1:160990146..160990789,3	K562	blood:
8	chr1:160964619..160967227-chr1:161147832..161149924,2	K562	blood:
9	chr1:160965718..160967539-chr1:160977694..160979398,2	K562	blood:
10	chr1:160966815..160967738-chr1:161109054..161109807,2	K562	blood:
11	chr1:160964763..160967593-chr1:161005630..161008574,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000215845	Chromatin interaction
ENSG00000270149	Chromatin interaction
ENSG00000158769	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs1062826	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.91[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1062827	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.91[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11265540	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11265542	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11799478	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11799521	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11801586	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11801591	0.85[CEU][hapmap];0.92[CHB][hapmap];0.82[JPT][hapmap]
rs11802727	0.82[JPT][hapmap]
rs11805856	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11807930	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.91[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12401336	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12403334	1.00[ASW][hapmap];0.94[CHB][hapmap];0.85[CHD][hapmap];0.90[GIH][hapmap];0.82[JPT][hapmap];0.91[LWK][hapmap];0.89[MEX][hapmap];0.89[TSI][hapmap];0.82[YRI][hapmap]
rs12405782	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12408778	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12565932	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.91[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17384360	0.94[CHB][hapmap]
rs17388108	0.96[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1806774	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2073655	0.87[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.86[GIH][hapmap];0.91[LWK][hapmap];0.94[MEX][hapmap];0.97[MKK][hapmap];0.92[TSI][hapmap];0.85[AMR][1000 genomes]
rs2073656	0.87[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];0.94[MEX][hapmap];0.97[MKK][hapmap];0.92[TSI][hapmap];0.87[AMR][1000 genomes]
rs2073658	0.87[AMR][1000 genomes]
rs2243427	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2247459	0.96[CEU][hapmap];0.93[CHB][hapmap];0.86[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2247596	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2247671	0.96[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2247790	0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.93[JPT][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2251597	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2251728	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2297219	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2297220	0.95[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2297221	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.91[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2297222	0.91[CEU][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2481080	0.96[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2481081	0.96[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2481083	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2481084	0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2481085	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2483145	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2774274	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2988726	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3119321	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3737785	0.91[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.82[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3737787	0.91[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.92[TSI][hapmap];0.86[AMR][1000 genomes]
rs41267947	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs41267949	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs41267951	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs41269993	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4339888	0.94[AMR][1000 genomes]
rs55728374	0.82[AMR][1000 genomes]
rs61802231	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61803664	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61803665	0.80[AFR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61803671	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61803672	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72712854	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs812741	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs836	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs869985	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.91[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]

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	nsv530077	chr1:160836448-161284904	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
2	nsv548058	chr1:160925455-160989614	Flanking Active TSS Genic enhancers Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1044478	F11R	Cis_1M	lymphoblastoid	RTeQTL
rs1044478	OR6N2	cis	parietal	SCAN
rs1044478	ARHGEF11	cis	cerebellum	SCAN
rs1044478	ROBLD3	cis	cerebellum	SCAN
rs1044478	ISG20L2	cis	cerebellum	SCAN

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:160948600-160968000	Weak transcription	Ovary	ovary
2	chr1:160952200-160967000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr1:160953800-160968200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr1:160957400-160967000	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr1:160957800-160968000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr1:160960000-160967200	Weak transcription	Primary B cells from cord blood	blood
7	chr1:160960000-160967400	Weak transcription	Lung	lung
8	chr1:160960000-160968000	Weak transcription	Pancreas	Pancrea
9	chr1:160960000-160970200	Weak transcription	Right Ventricle	heart
10	chr1:160960200-160967000	Weak transcription	Placenta	Placenta
11	chr1:160960200-160967600	Weak transcription	Fetal Muscle Trunk	muscle
12	chr1:160960200-160967600	Weak transcription	Fetal Muscle Leg	muscle
13	chr1:160960200-160968000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr1:160960200-160968400	Weak transcription	Left Ventricle	heart
15	chr1:160960400-160967000	Weak transcription	Fetal Intestine Small	intestine
16	chr1:160960400-160967600	Weak transcription	Fetal Stomach	stomach
17	chr1:160960400-160968000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr1:160960400-160968200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr1:160960400-160968200	Weak transcription	Fetal Brain Female	brain
20	chr1:160960400-160978400	Weak transcription	Fetal Lung	lung
21	chr1:160960600-160967000	Weak transcription	Fetal Thymus	thymus
22	chr1:160960600-160967000	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr1:160960600-160967000	Weak transcription	Stomach Mucosa	stomach
24	chr1:160960600-160967000	Weak transcription	GM12878-XiMat	blood
25	chr1:160960600-160967000	Weak transcription	Monocytes-CD14+_RO01746	blood
26	chr1:160960600-160967200	Weak transcription	Primary monocytes fromperipheralblood	blood
27	chr1:160960600-160967200	Weak transcription	HepG2	liver
28	chr1:160960600-160967400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr1:160960600-160967600	Weak transcription	Primary T cells from cord blood	blood
30	chr1:160960600-160968000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr1:160960600-160968000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr1:160960600-160968000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr1:160960600-160968000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr1:160960600-160968000	Weak transcription	Thymus	Thymus
35	chr1:160960600-160968400	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr1:160960600-160968600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr1:160960600-160968800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
38	chr1:160960600-160968800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr1:160960600-160968800	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr1:160960600-160968800	Weak transcription	Rectal Smooth Muscle	rectum
41	chr1:160960600-160969000	Weak transcription	Dnd41	blood
42	chr1:160960600-160969600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr1:160960600-160977400	Weak transcription	Fetal Kidney	kidney
44	chr1:160960600-160981600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr1:160960800-160967000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
46	chr1:160962600-160968000	Weak transcription	Spleen	Spleen
47	chr1:160963400-160983000	Weak transcription	HSMMtube	muscle
48	chr1:160963600-160967000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr1:160963600-160967000	Weak transcription	Fetal Heart	heart
50	chr1:160963800-160967000	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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