Variant report

Variant	rs4656934
Chromosome Location	chr1:160782742-160782743
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:160777120..160779933-chr1:160780615..160783432,4	K562	blood:
2	chr1:160776649..160779858-chr1:160780478..160783432,4	K562	blood:

Variant related genes	Relation type
ENSG00000122224	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs11265484	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11265485	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12072397	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12072399	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1333064	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2769587	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34002161	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4656931	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs482921	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs501026	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs501137	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs506263	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs508578	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs512197	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs520316	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs527253	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs527766	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs535241	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs536015	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs540224	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs546669	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs560681	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs575217	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs579589	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6427544	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6427545	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6656939	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6691072	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7541298	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7553107	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7555286	0.88[EUR][1000 genomes]
rs790624	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][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	esv1822379	chr1:160545332-160831143	Enhancers Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv464161	chr1:160747615-160852046	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv548057	chr1:160747615-160852046	Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4656934	LY9	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:160771000-160806600	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr1:160775600-160783000	Weak transcription	Duodenum Mucosa	Duodenum
3	chr1:160777400-160789000	Strong transcription	Primary B cells from cord blood	blood
4	chr1:160777600-160783400	Weak transcription	Gastric	stomach
5	chr1:160778000-160782800	Weak transcription	GM12878-XiMat	blood
6	chr1:160778000-160783000	Weak transcription	Fetal Thymus	thymus
7	chr1:160778000-160783000	Weak transcription	Thymus	Thymus
8	chr1:160778000-160783800	Weak transcription	Spleen	Spleen
9	chr1:160778000-160795600	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr1:160778000-160798400	Strong transcription	Primary B cells from peripheral blood	blood
11	chr1:160778400-160783200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr1:160778400-160799600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr1:160778600-160783200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr1:160779800-160789200	Strong transcription	Primary T cells from cord blood	blood
15	chr1:160780000-160789800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr1:160780800-160782800	Weak transcription	NHEK	skin
17	chr1:160780800-160787800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr1:160781000-160782800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr1:160781000-160783200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr1:160781000-160787600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr1:160781000-160789000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr1:160781200-160783000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr1:160781600-160787800	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr1:160781800-160782800	Strong transcription	Primary T killer memory cells from peripheral blood	blood
25	chr1:160782000-160782800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr1:160782000-160782800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr1:160782000-160783000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr1:160782000-160783400	Strong transcription	Primary T helper cells fromperipheralblood	blood
29	chr1:160782400-160782800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr1:160782400-160798200	Strong transcription	Primary T helper cells PMA-I stimulated	--
31	chr1:160782600-160783800	Genic enhancers	Primary T cells fromperipheralblood	blood
32	chr1:160782600-160803200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood

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