Variant report

Variant	rs2527687
Chromosome Location	chr7:2838485-2838486
allele	A/C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:10)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:10 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SPI1	chr7:2838358-2838642	GM12891	blood:	n/a	n/a
2	SPI1	chr7:2838440-2838570	GM12878	blood:	n/a	n/a
3	SPI1	chr7:2838435-2838574	K562	blood:	n/a	n/a
4	SPI1	chr7:2838308-2838785	HL-60	blood:	n/a	n/a
5	SPI1	chr7:2838381-2838633	GM12878	blood:	n/a	n/a
6	TBL1XR1	chr7:2838455-2838530	GM12878	blood:	n/a	n/a
7	SPI1	chr7:2838321-2838596	GM12891	blood:	n/a	n/a
8	CUX1	chr7:2838373-2838562	GM12878	blood:	n/a	n/a
9	SPI1	chr7:2838431-2838592	K562	blood:	n/a	n/a
10	SPI1	chr7:2838382-2838715	HL-60	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:2838034..2839572-chr7:2912043..2913829,2	MCF-7	breast:
2	chr7:2837950..2839626-chr7:2864748..2866453,2	MCF-7	breast:
3	chr7:2836297..2839698-chr7:2841908..2844688,4	K562	blood:
4	chr7:2834982..2836985-chr7:2838471..2841114,3	MCF-7	breast:
5	chr7:2837885..2839516-chr7:2842777..2844546,2	MCF-7	breast:

No data

Variant related genes	Relation type
GNA12	TF binding region

Extended variants
information (count: 94 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs1182173	0.82[AMR][1000 genomes]
rs1182175	0.92[CEU][hapmap];0.83[CHB][hapmap];0.81[CHD][hapmap];0.83[MEX][hapmap];0.82[AMR][1000 genomes]
rs1182177	0.83[CHB][hapmap];0.85[JPT][hapmap]
rs1182179	0.83[CHB][hapmap];0.85[CHD][hapmap]
rs1182180	0.83[AMR][1000 genomes]
rs1182181	0.83[CHB][hapmap];0.81[CHD][hapmap];0.85[JPT][hapmap]
rs1182184	0.83[JPT][hapmap]
rs1182185	0.83[CHB][hapmap]
rs1182188	0.83[CHB][hapmap];0.85[CHD][hapmap];0.85[JPT][hapmap]
rs1182189	0.83[CHB][hapmap];0.85[JPT][hapmap]
rs1182190	0.88[CEU][hapmap];0.83[CHB][hapmap];0.84[CHD][hapmap];0.86[GIH][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap];0.85[AMR][1000 genomes]
rs1182191	0.88[CEU][hapmap];0.83[CHB][hapmap];0.84[JPT][hapmap];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1182192	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1182193	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1182194	0.88[CEU][hapmap];0.83[CHB][hapmap];0.85[AMR][1000 genomes]
rs1182195	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1182196	0.96[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1182198	0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1182199	0.91[ASN][1000 genomes]
rs1182207	0.83[ASN][1000 genomes]
rs1182208	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1182209	0.96[CEU][hapmap];0.94[CHB][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1183085	0.85[JPT][hapmap]
rs13243214	0.89[ASN][1000 genomes]
rs1636264	0.94[CHB][hapmap];0.88[CHD][hapmap];0.92[JPT][hapmap];0.85[ASN][1000 genomes]
rs1713919	0.94[CHB][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs1713920	0.88[CEU][hapmap];0.83[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2107964	0.94[CHB][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs2158694	1.00[CHB][hapmap];0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs2248390	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2251491	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2260230	1.00[CHB][hapmap];0.92[JPT][hapmap];0.91[ASN][1000 genomes]
rs2266922	0.88[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2283779	0.91[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2283783	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2283784	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2527683	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2527684	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.93[MKK][hapmap];0.91[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2527690	0.95[CEU][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2527692	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2527694	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2527695	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2527696	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2533878	0.85[CHD][hapmap];0.85[JPT][hapmap]
rs2533879	0.94[ASN][1000 genomes]
rs2533882	0.96[ASN][1000 genomes]
rs2533884	0.85[ASN][1000 genomes]
rs2533886	0.82[MKK][hapmap]
rs2533888	0.81[LWK][hapmap];0.81[MKK][hapmap]
rs2644274	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2644275	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2644294	0.91[ASN][1000 genomes]
rs2644295	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2644296	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2644297	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2644298	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2644312	0.94[CHB][hapmap];0.92[JPT][hapmap];0.99[ASN][1000 genomes]
rs35957220	0.88[ASN][1000 genomes]
rs6970963	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6978692	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs757791	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.93[JPT][hapmap];0.84[MEX][hapmap];0.82[TSI][hapmap];0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7777484	0.92[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7807978	0.88[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];0.94[GIH][hapmap];0.93[JPT][hapmap];0.81[TSI][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs798480	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs798481	0.81[EUR][1000 genomes]
rs798482	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs798485	0.94[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs798486	0.94[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs798487	0.85[ASN][1000 genomes]
rs798488	0.89[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs798490	0.89[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs798491	0.80[CHB][hapmap];1.00[JPT][hapmap]
rs798492	0.89[CEU][hapmap];0.80[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];0.93[JPT][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap];0.84[EUR][1000 genomes]
rs798494	0.80[CHB][hapmap];1.00[JPT][hapmap]
rs798495	0.80[CHB][hapmap];1.00[JPT][hapmap]
rs798497	0.80[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs798498	0.85[CHB][hapmap];0.93[JPT][hapmap]
rs798499	0.88[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs798500	0.85[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs798503	0.84[CEU][hapmap];0.94[GIH][hapmap];0.87[MEX][hapmap];0.81[EUR][1000 genomes]
rs798512	0.84[CEU][hapmap];0.84[CHB][hapmap];0.86[JPT][hapmap]
rs798513	0.80[EUR][1000 genomes]
rs798518	0.85[CHB][hapmap];0.92[JPT][hapmap]
rs798528	0.85[CHB][hapmap];0.93[JPT][hapmap]
rs798548	0.85[CHD][hapmap]
rs798554	0.85[CHD][hapmap]
rs798557	0.88[CHB][hapmap]
rs960273	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1029250	chr7:2722737-2881021	Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv538652	chr7:2722737-2881021	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv1015700	chr7:2753965-2945848	Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	nsv1022612	chr7:2789555-3019200	Enhancers ZNF genes & repeats Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv1018162	chr7:2817460-2891181	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
6	nsv538655	chr7:2817460-2891181	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2527687		cis	Lymphoblastoid	GTEx
rs2527687	GNA12	cis	lymphoblastoid	seeQTL
rs2527687	HEATR2	cis	cerebellum	SCAN
rs2527687	GNA12	Cis_1M	lymphoblastoid	RTeQTL
rs2527687	GNA12	cis	multi-tissue	Pritchard
rs2527687	LOC392620	cis	multi-tissue	Pritchard
rs2527687	GNA12	cis	Nerve Tibial	GTEx
rs2527687	NUDT1	cis	parietal	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:2810600-2842600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr7:2810800-2840800	Weak transcription	Stomach Mucosa	stomach
3	chr7:2814400-2838800	Weak transcription	K562	blood
4	chr7:2815800-2840600	Weak transcription	Fetal Brain Male	brain
5	chr7:2822600-2841000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr7:2824000-2842800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr7:2829800-2841200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr7:2829800-2841400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr7:2830000-2841200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr7:2830200-2842800	Weak transcription	Colonic Mucosa	Colon
11	chr7:2832000-2841400	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr7:2832800-2841000	Weak transcription	NHEK	skin
13	chr7:2832800-2842600	Weak transcription	Rectal Smooth Muscle	rectum
14	chr7:2833000-2840600	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr7:2833000-2840800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr7:2833000-2842400	Weak transcription	Spleen	Spleen
17	chr7:2833200-2840800	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr7:2833200-2842400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr7:2834000-2840600	Weak transcription	Esophagus	oesophagus
20	chr7:2834000-2840800	Weak transcription	HMEC	breast
21	chr7:2834200-2840000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr7:2834200-2840800	Weak transcription	Colon Smooth Muscle	Colon
23	chr7:2834200-2841000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr7:2834200-2841200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr7:2834600-2838800	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr7:2834600-2840200	Weak transcription	Fetal Brain Female	brain
27	chr7:2834600-2840200	Weak transcription	Fetal Thymus	thymus
28	chr7:2834600-2840800	Weak transcription	Hela-S3	cervix
29	chr7:2834600-2840800	Weak transcription	Monocytes-CD14+_RO01746	blood
30	chr7:2834600-2841000	Weak transcription	Duodenum Mucosa	Duodenum
31	chr7:2834600-2841400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr7:2834600-2842400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr7:2834600-2847800	Weak transcription	Liver	Liver
34	chr7:2834800-2839000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr7:2834800-2839000	Weak transcription	GM12878-XiMat	blood
36	chr7:2834800-2839400	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr7:2834800-2840200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr7:2834800-2840400	Weak transcription	Fetal Intestine Small	intestine
39	chr7:2834800-2840800	Weak transcription	Primary T cells fromperipheralblood	blood
40	chr7:2834800-2840800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr7:2834800-2841000	Weak transcription	Primary T helper cells fromperipheralblood	blood
42	chr7:2834800-2841000	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr7:2834800-2841000	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr7:2834800-2841400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr7:2834800-2842200	Weak transcription	Brain Germinal Matrix	brain
46	chr7:2834800-2842400	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr7:2835000-2838600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
48	chr7:2835000-2838800	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr7:2835000-2839400	Weak transcription	Dnd41	blood
50	chr7:2835000-2839600	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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