Variant report

Variant	rs874224
Chromosome Location	chr15:76631797-76631798
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:11)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SPI1	chr15:76631402-76631856	HL-60	blood:	n/a	n/a
2	POLR2A	chr15:76631682-76632446	HL-60	blood:	n/a	n/a
3	POLR2A	chr15:76628957-76633759	H1-neurons	neurons:	n/a	n/a
4	MXI1	chr15:76627471-76631959	SK-N-SH	brain:	n/a	n/a
5	JUN	chr15:76627963-76631858	K562	blood:	n/a	chr15:76628895-76628904
6	POLR2A	chr15:76631377-76633541	H1-neurons	neurons:	n/a	n/a
7	SUZ12	chr15:76628987-76637136	NT2-D1	testis:	n/a	n/a
8	SPI1	chr15:76631355-76632136	HL-60	blood:	n/a	n/a
9	ZNF263	chr15:76627921-76631912	HEK293-T-REx	kidney:	n/a	n/a
10	CTBP2	chr15:76631455-76635500	H1-hESC	embryonic stem cell:	n/a	n/a
11	SUZ12	chr15:76629195-76634787	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:76601310..76610583-chr15:76618699..76634643,40	K562	blood:
2	chr15:76628671..76632944-chr15:76633969..76642252,10	MCF-7	breast:
3	chr15:76574110..76576498-chr15:76629872..76632197,2	K562	blood:
4	chr15:76601574..76614388-chr15:76623703..76634730,38	K562	blood:
5	chr15:76627980..76632315-chr15:76633215..76636196,5	MCF-7	breast:
6	chr15:76630323..76632934-chr15:77355490..77357171,2	K562	blood:
7	chr15:76630618..76633246-chr15:76671829..76673785,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000270036	TF binding region
ENSG00000259514	Chromatin interaction
ENSG00000270036	Chromatin interaction
ENSG00000140374	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs11858964	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs157760	0.87[CEU][hapmap];0.90[CHB][hapmap];1.00[MEX][hapmap]
rs157761	0.87[CEU][hapmap];0.89[CHB][hapmap]
rs157763	0.80[CHB][hapmap]
rs157766	0.80[CHB][hapmap]
rs157777	0.87[CEU][hapmap];0.90[CHB][hapmap]
rs157778	0.87[CEU][hapmap];0.90[CHB][hapmap]
rs157779	0.80[CHB][hapmap]
rs157789	0.87[CEU][hapmap];0.89[CHB][hapmap]
rs1801591	0.87[CEU][hapmap]
rs1810348	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs182253	0.87[CEU][hapmap];0.90[CHB][hapmap];1.00[MEX][hapmap]
rs2078437	0.87[CEU][hapmap];0.90[CHB][hapmap];1.00[MEX][hapmap]
rs2291449	0.87[CEU][hapmap]
rs2456033	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2456040	0.82[EUR][1000 genomes]
rs2456042	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2456047	0.83[AMR][1000 genomes]
rs2456054	0.84[YRI][hapmap]
rs2456063	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2456066	1.00[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2456067	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2456070	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2456072	0.87[YRI][hapmap]
rs2456074	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2460151	0.85[YRI][hapmap]
rs2460153	1.00[CEU][hapmap];0.93[YRI][hapmap];0.83[AMR][1000 genomes]
rs2460155	0.82[YRI][hapmap]
rs2460158	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs2460161	0.87[CEU][hapmap];0.90[CHB][hapmap];1.00[MEX][hapmap]
rs2469211	1.00[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2469212	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2469214	1.00[CEU][hapmap];0.91[TSI][hapmap];0.87[EUR][1000 genomes]
rs2469215	1.00[CEU][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2469216	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2469533	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2469538	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2469539	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2469552	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2469554	0.87[CEU][hapmap];0.90[CHB][hapmap]
rs2469564	0.93[ASW][hapmap];0.88[CEU][hapmap];0.90[LWK][hapmap];0.85[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes]
rs2469568	0.95[YRI][hapmap];0.83[AMR][1000 genomes]
rs2469573	1.00[CEU][hapmap];0.87[YRI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs283796	0.87[CEU][hapmap];0.90[CHB][hapmap]
rs283802	0.87[CEU][hapmap];0.89[CHB][hapmap]
rs284898	0.87[CEU][hapmap];0.90[CHB][hapmap];1.00[MEX][hapmap]
rs284902	0.87[CEU][hapmap];0.89[CHB][hapmap]
rs284903	0.87[CEU][hapmap];0.90[CHB][hapmap];1.00[MEX][hapmap]
rs284904	0.87[CEU][hapmap];0.90[CHB][hapmap];1.00[MEX][hapmap]
rs284905	0.87[CEU][hapmap];0.90[CHB][hapmap]
rs284907	0.87[CEU][hapmap];0.90[CHB][hapmap];1.00[MEX][hapmap]
rs2956875	1.00[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2957037	0.83[YRI][hapmap]
rs2957560	0.88[CHB][hapmap];0.84[JPT][hapmap]
rs2957607	0.87[CEU][hapmap];0.90[CHB][hapmap];1.00[MEX][hapmap]
rs2957613	0.87[CEU][hapmap]
rs2959846	0.80[EUR][1000 genomes]
rs387321	0.87[CEU][hapmap];0.90[CHB][hapmap];0.82[JPT][hapmap]
rs4489970	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4636879	0.82[CHB][hapmap];0.82[ASN][1000 genomes]
rs480672	0.90[CHB][hapmap]
rs4886490	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4886491	0.87[CEU][hapmap];0.90[CHB][hapmap]
rs4886492	0.86[CEU][hapmap];0.90[CHB][hapmap]
rs494268	0.87[CEU][hapmap];0.90[CHB][hapmap]
rs506000	0.87[CEU][hapmap];0.90[CHB][hapmap]
rs6495200	0.88[EUR][1000 genomes]
rs7180257	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8031378	0.87[CEU][hapmap];0.90[CHB][hapmap]
rs8031672	0.82[CEU][hapmap]
rs8042255	1.00[CEU][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes]
rs874223	1.00[EUR][1000 genomes];1.00[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	nsv904399	chr15:76622903-76646575	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv827391	chr15:76626571-76636327	Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	esv3398970	chr15:76629522-76632070	Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs874224	HPCA	trans	brain	seeQTL
rs874224	ISL2	cis	lymphoblastoid	seeQTL
rs874224	ISL2	cis	multi-tissue	Pritchard
rs874224	ISL2	cis	Whole Blood	GTEx

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:76627400-76635400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
2	chr15:76627600-76632400	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
3	chr15:76627600-76634400	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
4	chr15:76628000-76631800	Bivalent/Poised TSS	Fetal Stomach	stomach
5	chr15:76628000-76632000	Bivalent/Poised TSS	Fetal Intestine Small	intestine
6	chr15:76629000-76633600	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
7	chr15:76629200-76632200	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
8	chr15:76629200-76632200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
9	chr15:76629200-76632600	Bivalent Enhancer	Fetal Thymus	thymus
10	chr15:76629400-76632000	Bivalent Enhancer	Primary B cells from peripheral blood	blood
11	chr15:76629400-76633400	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
12	chr15:76629600-76632000	Bivalent Enhancer	Spleen	Spleen
13	chr15:76629600-76632200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
14	chr15:76629800-76631800	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
15	chr15:76629800-76632800	Bivalent Enhancer	Stomach Mucosa	stomach
16	chr15:76630000-76632200	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
17	chr15:76630200-76632200	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
18	chr15:76630200-76632200	Bivalent/Poised TSS	Fetal Intestine Large	intestine
19	chr15:76630200-76641800	Weak transcription	A549	lung
20	chr15:76630400-76632600	Bivalent/Poised TSS	Colon Smooth Muscle	Colon
21	chr15:76630400-76636400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr15:76630600-76632200	Bivalent Enhancer	Brain Hippocampus Middle	brain
23	chr15:76630600-76632400	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
24	chr15:76630600-76635600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr15:76630800-76631800	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
26	chr15:76630800-76632000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
27	chr15:76630800-76632000	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr15:76630800-76632000	Bivalent Enhancer	Adipose Nuclei	Adipose
29	chr15:76630800-76632000	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
30	chr15:76630800-76632200	Enhancers	Pancreas	Pancrea
31	chr15:76630800-76632200	Weak transcription	HSMMtube	muscle
32	chr15:76630800-76632400	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr15:76631000-76631800	Flanking Active TSS	HepG2	liver
34	chr15:76631000-76631800	Transcr. at gene 5' and 3'	K562	blood
35	chr15:76631000-76632000	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr15:76631000-76632200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr15:76631000-76632200	Enhancers	Right Ventricle	heart
38	chr15:76631000-76632600	Bivalent Enhancer	Liver	Liver
39	chr15:76631200-76632000	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
40	chr15:76631200-76632000	Bivalent Enhancer	H9 Cell Line	embryonic stem cell
41	chr15:76631200-76632000	Bivalent Enhancer	Duodenum Mucosa	Duodenum
42	chr15:76631200-76632000	Bivalent Enhancer	Rectal Mucosa Donor 31	rectum
43	chr15:76631200-76632000	Weak transcription	HSMM	muscle
44	chr15:76631200-76632200	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr15:76631200-76632200	Bivalent Enhancer	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr15:76631200-76632200	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
47	chr15:76631200-76632200	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
48	chr15:76631200-76632200	Bivalent Enhancer	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr15:76631200-76632200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr15:76631200-76632200	Enhancers	Gastric	stomach

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