Variant report

Variant	rs4656271
Chromosome Location	chr1:160782942-160782943
allele	A/G
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	JUND	chr1:160782907-160783588	HCT-116	colon:	n/a	chr1:160783215-160783226
2	FOSL2	chr1:160782938-160783460	MCF-7	breast:	n/a	n/a
3	JUN	chr1:160782887-160783504	K562	blood:	n/a	n/a
4	TCF12	chr1:160782853-160783587	A549	lung:	n/a	n/a
5	EP300	chr1:160782865-160783510	A549	lung:	n/a	n/a
6	JUND	chr1:160782873-160783559	HCT-116	colon:	n/a	chr1:160783215-160783226
7	CBX3	chr1:160782865-160783460	HCT-116	colon:	n/a	n/a
8	SP1	chr1:160782898-160783553	HCT-116	colon:	n/a	n/a
9	SP1	chr1:160782897-160783452	A549	lung:	n/a	n/a
10	FOSL1	chr1:160782771-160783631	HCT-116	colon:	n/a	chr1:160783215-160783226
11	SP1	chr1:160782906-160783444	A549	lung:	n/a	n/a
12	FOSL1	chr1:160782871-160783600	HCT-116	colon:	n/a	chr1:160783215-160783226
13	FOSL2	chr1:160782820-160783553	A549	lung:	n/a	n/a
14	EP300	chr1:160782929-160783406	A549	lung:	n/a	n/a

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
LY9	TF binding region
ENSG00000122224	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11265492	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12117689	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12128261	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12143580	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1556517	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1961611	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2271967	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35132864	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3817407	0.96[EUR][1000 genomes]
rs4656270	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4656932	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4656933	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4656942	0.91[AFR][1000 genomes]
rs474918	0.99[AMR][1000 genomes];0.97[EUR][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
rs4656271	SLAMF7	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:36 , 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	chr1:160778000-160783000	Weak transcription	Fetal Thymus	thymus
6	chr1:160778000-160783000	Weak transcription	Thymus	Thymus
7	chr1:160778000-160783800	Weak transcription	Spleen	Spleen
8	chr1:160778000-160795600	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr1:160778000-160798400	Strong transcription	Primary B cells from peripheral blood	blood
10	chr1:160778400-160783200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr1:160778400-160799600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr1:160778600-160783200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr1:160779800-160789200	Strong transcription	Primary T cells from cord blood	blood
14	chr1:160780000-160789800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr1:160780800-160787800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr1:160781000-160783200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr1:160781000-160787600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr1:160781000-160789000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr1:160781200-160783000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr1:160781600-160787800	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr1:160782000-160783000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr1:160782000-160783400	Strong transcription	Primary T helper cells fromperipheralblood	blood
23	chr1:160782400-160798200	Strong transcription	Primary T helper cells PMA-I stimulated	--
24	chr1:160782600-160783800	Genic enhancers	Primary T cells fromperipheralblood	blood
25	chr1:160782600-160803200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr1:160782800-160783000	Enhancers	A549	lung
27	chr1:160782800-160783400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
28	chr1:160782800-160783400	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
29	chr1:160782800-160783600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr1:160782800-160783600	Enhancers	GM12878-XiMat	blood
31	chr1:160782800-160783600	Enhancers	HMEC	breast
32	chr1:160782800-160783800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr1:160782800-160784000	Enhancers	NHEK	skin
34	chr1:160782800-160784200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr1:160782800-160789200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
36	chr1:160782800-160789600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood

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