Variant report

Variant	rs2297221
Chromosome Location	chr1:160970968-160970969
allele	C/T
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	POLR2A	chr1:160970908-160971134	K562	blood:	n/a	n/a
2	POLR2A	chr1:160970390-160971572	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:160969057..160971514-chr1:161037864..161040165,2	K562	blood:

Variant related genes	Relation type
F11R	TF binding region
ENSG00000186517	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs1044478	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]
rs1062826	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1062827	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11265540	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11265542	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11799478	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11799521	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11801586	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11801591	0.90[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap]
rs11802727	0.83[CEU][hapmap];0.93[JPT][hapmap]
rs11805856	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11807930	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12401336	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12403334	1.00[ASW][hapmap];0.94[CHB][hapmap];0.85[CHD][hapmap];0.90[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.82[YRI][hapmap]
rs12405782	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12408778	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12565932	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17384360	0.94[CHB][hapmap]
rs17388108	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1806774	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2073655	0.91[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.86[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];0.92[TSI][hapmap];0.86[AMR][1000 genomes]
rs2073656	0.91[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.97[MKK][hapmap];0.92[TSI][hapmap];0.89[AMR][1000 genomes]
rs2073658	0.89[AMR][1000 genomes]
rs2243427	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2247459	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2247596	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2247671	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2247790	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2251597	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2251728	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2255852	0.81[JPT][hapmap]
rs2265243	0.83[ASN][1000 genomes]
rs2297219	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2297220	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];1.00[ASN][1000 genomes]
rs2297222	0.91[CEU][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]
rs2481080	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2481081	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2481083	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2481084	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2481085	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2483145	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2774274	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2988726	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3119321	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3737785	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3737787	0.87[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.97[MKK][hapmap];0.92[TSI][hapmap];0.87[AMR][1000 genomes]
rs41267947	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs41267949	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs41267951	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs41269993	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4339888	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs55728374	0.83[AMR][1000 genomes]
rs61802231	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61803664	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61803665	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61803671	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61803672	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72712854	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs812741	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs836	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs869985	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2297221	ROBLD3	cis	cerebellum	SCAN
rs2297221	OR10J5	cis	cerebellum	SCAN
rs2297221	F11R	Cis_1M	lymphoblastoid	RTeQTL
rs2297221	ARHGEF11	cis	cerebellum	SCAN
rs2297221	ISG20L2	cis	cerebellum	SCAN
rs2297221	PEAR1	cis	parietal	SCAN

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:160960400-160978400	Weak transcription	Fetal Lung	lung
2	chr1:160960600-160977400	Weak transcription	Fetal Kidney	kidney
3	chr1:160960600-160981600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr1:160963400-160983000	Weak transcription	HSMMtube	muscle
5	chr1:160964400-160972600	Strong transcription	HUES48 Cell Line	embryonic stem cell
6	chr1:160965000-160971800	Strong transcription	H1 Cell Line	embryonic stem cell
7	chr1:160965400-160972600	Strong transcription	HUES64 Cell Line	embryonic stem cell
8	chr1:160966400-160971000	Weak transcription	Psoas Muscle	Psoas
9	chr1:160966600-160971800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr1:160966600-160971800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
11	chr1:160966800-160971200	Strong transcription	Sigmoid Colon	Sigmoid Colon
12	chr1:160966800-160972600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
13	chr1:160967000-160971200	Strong transcription	Fetal Thymus	thymus
14	chr1:160967000-160971600	Strong transcription	Esophagus	oesophagus
15	chr1:160967000-160971800	Strong transcription	H9 Cell Line	embryonic stem cell
16	chr1:160967000-160971800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
17	chr1:160967000-160972400	Strong transcription	Rectal Mucosa Donor 29	rectum
18	chr1:160967400-160971200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr1:160967400-160972400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr1:160967600-160971000	Strong transcription	Primary monocytes fromperipheralblood	blood
21	chr1:160967600-160971000	Strong transcription	Placenta Amnion	Placenta Amnion
22	chr1:160967600-160971000	Strong transcription	GM12878-XiMat	blood
23	chr1:160967600-160971400	Strong transcription	Primary B cells from cord blood	blood
24	chr1:160967600-160971400	Strong transcription	Primary hematopoietic stem cells	blood
25	chr1:160967600-160971600	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr1:160967600-160971800	Strong transcription	Primary neutrophils fromperipheralblood	blood
27	chr1:160967600-160971800	Strong transcription	Fetal Stomach	stomach
28	chr1:160967600-160971800	Strong transcription	NHEK	skin
29	chr1:160967600-160972200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
30	chr1:160967600-160972200	Strong transcription	Primary T cells from cord blood	blood
31	chr1:160967600-160972600	Strong transcription	HUES6 Cell Line	embryonic stem cell
32	chr1:160967800-160971200	Strong transcription	Adipose Nuclei	Adipose
33	chr1:160967800-160971200	Strong transcription	Stomach Smooth Muscle	stomach
34	chr1:160967800-160971400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
35	chr1:160967800-160971400	Weak transcription	Brain Substantia Nigra	brain
36	chr1:160967800-160971600	Weak transcription	Brain Anterior Caudate	brain
37	chr1:160967800-160971800	Strong transcription	Primary T helper cells fromperipheralblood	blood
38	chr1:160967800-160971800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr1:160967800-160971800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr1:160967800-160971800	Strong transcription	Rectal Mucosa Donor 31	rectum
41	chr1:160967800-160971800	Strong transcription	HMEC	breast
42	chr1:160967800-160978200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr1:160967800-160978800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr1:160968000-160971000	Strong transcription	Primary T cells fromperipheralblood	blood
45	chr1:160968000-160971000	Strong transcription	Lung	lung
46	chr1:160968000-160971000	Strong transcription	Ovary	ovary
47	chr1:160968000-160971000	Strong transcription	Thymus	Thymus
48	chr1:160968000-160971000	Strong transcription	HUVEC	blood vessel
49	chr1:160968000-160971200	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr1:160968000-160971200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood

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