Variant report

Variant	rs2644296
Chromosome Location	chr7:2859061-2859062
allele	A/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	EBF1	chr7:2858832-2859150	GM12878	blood:	n/a	n/a
2	POLR2A	chr7:2858971-2859345	MCF10A-Er-Src	breast:	n/a	n/a
3	SP1	chr7:2858849-2859256	GM12878	blood:	n/a	n/a
4	EP300	chr7:2858872-2859297	GM12878	blood:	n/a	chr7:2859127-2859136
5	RUNX3	chr7:2858773-2859414	GM12878	blood:	n/a	n/a
6	TCF12	chr7:2858933-2859199	GM12878	blood:	n/a	n/a
7	EP300	chr7:2858954-2859292	GM12878	blood:	n/a	chr7:2859127-2859136
8	EP300	chr7:2858878-2859564	GM12878	blood:	n/a	chr7:2859127-2859136
9	POU2F2	chr7:2858846-2859303	GM12878	blood:	n/a	n/a
10	EBF1	chr7:2858874-2859306	GM12878	blood:	n/a	n/a
11	BCL11A	chr7:2858907-2859179	GM12878	blood:	n/a	chr7:2859127-2859136
12	MYC	chr7:2859053-2859226	MCF10A-Er-Src	breast:	n/a	chr7:2859127-2859136
13	RELA	chr7:2858921-2859280	GM19099	blood:	n/a	n/a
14	FOS	chr7:2858950-2859299	MCF10A-Er-Src	breast:	n/a	chr7:2859126-2859135
15	FOS	chr7:2858955-2859305	MCF10A-Er-Src	breast:	n/a	chr7:2859126-2859135
16	FOS	chr7:2858948-2859306	MCF10A-Er-Src	breast:	n/a	chr7:2859126-2859135
17	BATF	chr7:2858902-2859218	GM12878	blood:	n/a	chr7:2859128-2859138
18	NFIC	chr7:2858856-2859393	GM12878	blood:	n/a	n/a
19	RUNX3	chr7:2858850-2859309	GM12878	blood:	n/a	n/a
20	TCF12	chr7:2858920-2859208	GM12878	blood:	n/a	n/a
21	BATF	chr7:2858928-2859195	GM12878	blood:	n/a	chr7:2859128-2859138
22	ZNF143	chr7:2859053-2859251	GM12878	blood:	n/a	n/a
23	EBF1	chr7:2858812-2859194	GM12878	blood:	n/a	n/a
24	FOS	chr7:2858935-2859355	MCF10A-Er-Src	breast:	n/a	chr7:2859126-2859135
25	IKZF1	chr7:2858945-2859605	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:2726641..2729918-chr7:2858663..2861748,4	MCF-7	breast:
2	chr7:2855867..2858678-chr7:2858785..2861343,3	MCF-7	breast:
3	chr7:2796001..2798506-chr7:2858838..2860975,2	MCF-7	breast:

Variant related genes	Relation type
GNA12	TF binding region
ENSG00000174945	Chromatin interaction

Extended variants
information (count: 92 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs1182173	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1182174	0.85[JPT][hapmap]
rs1182175	0.92[CEU][hapmap];0.83[CHB][hapmap];0.84[GIH][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.92[YRI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1182177	0.83[CHB][hapmap]
rs1182179	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs1182180	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1182181	0.83[CHB][hapmap]
rs1182185	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs1182188	0.83[CHB][hapmap]
rs1182189	0.83[CHB][hapmap]
rs1182190	0.82[ASW][hapmap];0.88[CEU][hapmap];0.83[CHB][hapmap];0.94[GIH][hapmap];0.86[JPT][hapmap];0.90[LWK][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1182191	0.88[CEU][hapmap];0.83[CHB][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1182192	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1182193	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1182194	0.88[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap];0.88[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1182195	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1182196	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1182197	0.85[JPT][hapmap]
rs1182198	0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1182199	0.96[ASN][1000 genomes]
rs1182208	0.93[JPT][hapmap];0.83[ASN][1000 genomes]
rs1182209	0.96[CEU][hapmap];0.94[CHB][hapmap];0.91[JPT][hapmap];0.91[YRI][hapmap];0.87[ASN][1000 genomes]
rs13243214	0.85[ASN][1000 genomes]
rs1636264	0.94[CHB][hapmap];0.89[CHD][hapmap];0.86[JPT][hapmap];0.88[YRI][hapmap];0.89[ASN][1000 genomes]
rs1713919	0.94[CHB][hapmap];0.85[ASN][1000 genomes]
rs1713920	0.88[CEU][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2107964	0.94[CHB][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs2158694	1.00[CHB][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs2248390	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2251491	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2260230	1.00[CHB][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs2266922	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2283779	0.91[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.84[ASN][1000 genomes]
rs2283783	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2283784	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2527683	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2527684	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.93[JPT][hapmap];0.92[MEX][hapmap];0.86[TSI][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2527687	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]
rs2527690	0.95[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2527692	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2527694	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2527695	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2527696	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2533879	0.95[ASN][1000 genomes]
rs2533882	0.93[ASN][1000 genomes]
rs2644274	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2644275	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2644294	0.87[ASN][1000 genomes]
rs2644295	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2644297	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2644298	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2644304	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2644306	0.88[YRI][hapmap]
rs2644312	0.94[CHB][hapmap];0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs35957220	0.84[ASN][1000 genomes]
rs6970963	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6978692	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs757786	0.92[YRI][hapmap]
rs757791	0.83[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap];0.88[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7777484	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7807978	0.88[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.88[ASN][1000 genomes]
rs798480	0.81[ASN][1000 genomes]
rs798482	0.81[ASN][1000 genomes]
rs798485	0.94[CHB][hapmap];0.93[CHD][hapmap];0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs798486	0.94[CHB][hapmap];0.96[CHD][hapmap];0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs798487	0.81[ASN][1000 genomes]
rs798488	0.89[CHB][hapmap];0.93[JPT][hapmap]
rs798490	0.89[CHB][hapmap];0.96[CHD][hapmap];0.93[JPT][hapmap]
rs798491	0.80[CHB][hapmap];0.93[JPT][hapmap]
rs798492	0.89[CEU][hapmap];0.80[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap]
rs798494	0.80[CHB][hapmap];0.93[JPT][hapmap]
rs798495	0.80[CHB][hapmap];0.93[JPT][hapmap]
rs798497	0.80[CHB][hapmap];0.93[CHD][hapmap];0.93[JPT][hapmap]
rs798498	0.85[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs798499	0.88[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap]
rs798500	0.85[CHB][hapmap];0.85[CHD][hapmap];0.93[JPT][hapmap]
rs798503	0.83[ASW][hapmap];0.84[CEU][hapmap];0.97[GIH][hapmap];0.83[LWK][hapmap];0.87[MEX][hapmap];0.88[YRI][hapmap]
rs798512	0.84[CEU][hapmap];0.84[CHB][hapmap];0.93[JPT][hapmap]
rs798518	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs798528	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs798548	0.86[CHD][hapmap];0.86[JPT][hapmap]
rs798554	0.86[CHD][hapmap];0.86[JPT][hapmap]
rs798556	0.86[JPT][hapmap]
rs798557	0.88[CHB][hapmap]
rs960273	1.00[CHB][hapmap];0.93[JPT][hapmap];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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
7	nsv1019463	chr7:2848448-2881872	Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2644296	GNA12	cis	Nerve Tibial	GTEx
rs2644296	GNA12	cis	multi-tissue	Pritchard
rs2644296	NUDT1	cis	parietal	SCAN
rs2644296		cis	Lymphoblastoid	GTEx
rs2644296	GNA12	cis	lymphoblastoid	seeQTL
rs2644296	HEATR2	cis	cerebellum	SCAN
rs2644296	FTSJ2	cis	lymphoblastoid	GTEx
rs2644296	LOC392620	cis	multi-tissue	Pritchard

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:2842600-2869400	Weak transcription	Primary T cells from cord blood	blood
2	chr7:2843000-2860800	Weak transcription	Esophagus	oesophagus
3	chr7:2843200-2860800	Weak transcription	HSMMtube	muscle
4	chr7:2843200-2864400	Weak transcription	Primary T cells fromperipheralblood	blood
5	chr7:2843600-2860600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr7:2843600-2864400	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr7:2845800-2862200	Weak transcription	K562	blood
8	chr7:2848400-2859400	Weak transcription	Fetal Intestine Large	intestine
9	chr7:2848600-2864000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr7:2848800-2863400	Weak transcription	Fetal Brain Female	brain
11	chr7:2848800-2874800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr7:2849400-2860800	Weak transcription	Stomach Mucosa	stomach
13	chr7:2849600-2866000	Enhancers	Placenta	Placenta
14	chr7:2851000-2860200	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr7:2851600-2860600	Weak transcription	Primary B cells from cord blood	blood
16	chr7:2851600-2861000	Weak transcription	Primary hematopoietic stem cells	blood
17	chr7:2851600-2861000	Weak transcription	Brain Cingulate Gyrus	brain
18	chr7:2851600-2869600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr7:2851800-2860400	Weak transcription	Monocytes-CD14+_RO01746	blood
20	chr7:2851800-2882800	Weak transcription	Aorta	Aorta
21	chr7:2852000-2860400	Weak transcription	Brain Hippocampus Middle	brain
22	chr7:2853200-2860600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr7:2854000-2874800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr7:2854600-2860600	Weak transcription	Fetal Kidney	kidney
25	chr7:2854600-2861000	Weak transcription	Duodenum Mucosa	Duodenum
26	chr7:2854800-2859200	Weak transcription	Small Intestine	intestine
27	chr7:2854800-2860200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr7:2854800-2860200	Weak transcription	Colonic Mucosa	Colon
29	chr7:2855400-2859400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr7:2855800-2860200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr7:2855800-2860800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr7:2855800-2860800	Weak transcription	Stomach Smooth Muscle	stomach
33	chr7:2855800-2863600	Weak transcription	Brain Angular Gyrus	brain
34	chr7:2857000-2859800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr7:2857000-2864600	Enhancers	H1 Cell Line	embryonic stem cell
36	chr7:2857000-2865000	Enhancers	Ovary	ovary
37	chr7:2857000-2867000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr7:2857200-2859200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr7:2857200-2859400	Enhancers	Duodenum Smooth Muscle	Duodenum
40	chr7:2857200-2859400	Enhancers	NHLF	lung
41	chr7:2857200-2860400	Enhancers	A549	lung
42	chr7:2857200-2861600	Enhancers	Skeletal Muscle Male	skeletal muscle
43	chr7:2857200-2861800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr7:2857200-2861800	Enhancers	Muscle Satellite Cultured Cells	--
45	chr7:2857200-2862000	Enhancers	Adipose Nuclei	Adipose
46	chr7:2857200-2862000	Enhancers	Colon Smooth Muscle	Colon
47	chr7:2857200-2864200	Enhancers	NHDF-Ad	bronchial
48	chr7:2857200-2865400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr7:2857400-2859800	Weak transcription	Pancreas	Pancrea
50	chr7:2857800-2859200	Weak transcription	Pancreatic Islets	Pancreatic Islet

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