Variant report

Variant	rs2644298
Chromosome Location	chr7:2858448-2858449
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:2857088..2858665-chr7:2859530..2861799,2	K562	blood:
2	chr7:2857314..2858833-chr7:2861762..2864042,2	MCF-7	breast:
3	chr7:2852817..2855372-chr7:2857055..2858634,2	MCF-7	breast:
4	chr7:2855867..2858678-chr7:2858785..2861343,3	MCF-7	breast:
5	chr7:2857161..2858928-chr7:2879727..2881596,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000146535	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs1182173	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1182175	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1182180	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1182190	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1182191	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1182192	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1182193	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1182194	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1182195	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1182196	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1182198	0.92[ASN][1000 genomes]
rs1182199	0.96[ASN][1000 genomes]
rs1182208	0.83[ASN][1000 genomes]
rs1182209	0.87[ASN][1000 genomes]
rs13243214	0.85[ASN][1000 genomes]
rs1636264	0.89[ASN][1000 genomes]
rs1713919	0.85[ASN][1000 genomes]
rs1713920	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2107964	0.90[ASN][1000 genomes]
rs2158694	0.89[ASN][1000 genomes]
rs2248390	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2251491	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2260230	0.87[ASN][1000 genomes]
rs2266922	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2283779	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2283783	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2283784	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2527683	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2527684	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2527687	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2527690	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2527692	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2527694	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2527695	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2527696	0.87[AFR][1000 genomes];0.97[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	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2644275	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2644294	0.87[ASN][1000 genomes]
rs2644295	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2644296	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2644297	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2644304	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2644312	0.92[ASN][1000 genomes]
rs35957220	0.84[ASN][1000 genomes]
rs6970963	0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6978692	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs757791	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7777484	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7807978	0.88[ASN][1000 genomes]
rs798480	0.81[ASN][1000 genomes]
rs798482	0.81[ASN][1000 genomes]
rs798485	0.81[ASN][1000 genomes]
rs798486	0.81[ASN][1000 genomes]
rs798487	0.81[ASN][1000 genomes]
rs798498	0.81[ASN][1000 genomes]
rs960273	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2644298	GNA12	cis	Nerve Tibial	GTEx
rs2644298	GNA12	Cis_1M	lymphoblastoid	RTeQTL

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	chr7:2844000-2858800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr7:2845800-2862200	Weak transcription	K562	blood
9	chr7:2847800-2858800	Weak transcription	HSMM	muscle
10	chr7:2848200-2858800	Weak transcription	NHEK	skin
11	chr7:2848400-2858800	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr7:2848400-2859400	Weak transcription	Fetal Intestine Large	intestine
13	chr7:2848600-2864000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr7:2848800-2858600	Weak transcription	Gastric	stomach
15	chr7:2848800-2863400	Weak transcription	Fetal Brain Female	brain
16	chr7:2848800-2874800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr7:2849400-2860800	Weak transcription	Stomach Mucosa	stomach
18	chr7:2849600-2866000	Enhancers	Placenta	Placenta
19	chr7:2851000-2860200	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr7:2851200-2858600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr7:2851600-2858600	Weak transcription	HMEC	breast
22	chr7:2851600-2858800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr7:2851600-2860600	Weak transcription	Primary B cells from cord blood	blood
24	chr7:2851600-2861000	Weak transcription	Primary hematopoietic stem cells	blood
25	chr7:2851600-2861000	Weak transcription	Brain Cingulate Gyrus	brain
26	chr7:2851600-2869600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr7:2851800-2860400	Weak transcription	Monocytes-CD14+_RO01746	blood
28	chr7:2851800-2882800	Weak transcription	Aorta	Aorta
29	chr7:2852000-2858600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr7:2852000-2858800	Weak transcription	Rectal Smooth Muscle	rectum
31	chr7:2852000-2860400	Weak transcription	Brain Hippocampus Middle	brain
32	chr7:2853200-2860600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr7:2853600-2858800	Weak transcription	Hela-S3	cervix
34	chr7:2853800-2858800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr7:2854000-2874800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr7:2854200-2858800	Weak transcription	Primary B cells from peripheral blood	blood
37	chr7:2854600-2860600	Weak transcription	Fetal Kidney	kidney
38	chr7:2854600-2861000	Weak transcription	Duodenum Mucosa	Duodenum
39	chr7:2854800-2858600	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr7:2854800-2859200	Weak transcription	Small Intestine	intestine
41	chr7:2854800-2860200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr7:2854800-2860200	Weak transcription	Colonic Mucosa	Colon
43	chr7:2855200-2858800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr7:2855400-2858600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
45	chr7:2855400-2858600	Enhancers	HepG2	liver
46	chr7:2855400-2858800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr7:2855400-2859400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr7:2855600-2858600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr7:2855800-2858600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
50	chr7:2855800-2858600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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