Variant report

Variant	rs2644274
Chromosome Location	chr7:2854380-2854381
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:2852392..2854635-chr7:2859767..2862192,2	K562	blood:

Extended variants
information (count: 88 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs1182173	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1182175	0.91[CEU][hapmap];0.83[CHB][hapmap];0.85[JPT][hapmap];0.95[YRI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1182179	0.83[CHB][hapmap];0.85[JPT][hapmap]
rs1182180	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1182181	0.83[CHB][hapmap]
rs1182188	0.83[CHB][hapmap]
rs1182190	0.86[CEU][hapmap];0.83[CHB][hapmap];0.85[JPT][hapmap];0.91[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1182191	0.87[CEU][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1182192	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1182193	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1182194	0.87[CEU][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1182195	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1182196	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1182197	0.80[CHB][hapmap]
rs1182198	0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1182199	0.97[ASN][1000 genomes]
rs1182208	0.93[JPT][hapmap];0.84[ASN][1000 genomes]
rs1182209	0.95[CEU][hapmap];0.94[CHB][hapmap];0.91[JPT][hapmap];0.95[YRI][hapmap];0.88[ASN][1000 genomes]
rs13243214	0.86[ASN][1000 genomes]
rs1636264	0.94[CHB][hapmap];0.85[JPT][hapmap];0.91[YRI][hapmap];0.90[ASN][1000 genomes]
rs1713919	0.94[CHB][hapmap];0.86[ASN][1000 genomes]
rs1713920	0.91[CEU][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2107964	0.94[CHB][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs2158694	1.00[CHB][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs2248390	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2251491	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2260230	1.00[CHB][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs2266922	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2283779	0.90[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2283783	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2283784	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2527683	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2527684	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2527687	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]
rs2527690	0.95[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2527692	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2527694	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2527695	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2527696	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2533879	0.94[ASN][1000 genomes]
rs2533882	0.94[ASN][1000 genomes]
rs2644275	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2644294	0.88[ASN][1000 genomes]
rs2644295	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2644296	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]
rs2644297	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2644298	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2644304	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2644306	0.92[YRI][hapmap]
rs2644312	0.94[CHB][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs35957220	0.85[ASN][1000 genomes]
rs6970963	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6978692	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs757786	0.96[YRI][hapmap]
rs757791	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7777484	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7807978	0.87[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs798480	0.82[ASN][1000 genomes]
rs798482	0.82[ASN][1000 genomes]
rs798485	0.94[CHB][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs798486	0.94[CHB][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs798487	0.82[ASN][1000 genomes]
rs798488	0.90[CHB][hapmap];0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs798490	0.89[CHB][hapmap];0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs798491	0.81[CHB][hapmap];0.93[JPT][hapmap]
rs798492	0.87[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs798494	0.81[CHB][hapmap];0.93[JPT][hapmap]
rs798495	0.81[CHB][hapmap];0.93[JPT][hapmap]
rs798497	0.80[CHB][hapmap];0.93[JPT][hapmap]
rs798498	0.85[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs798499	0.86[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs798500	0.85[CHB][hapmap];0.93[JPT][hapmap]
rs798503	0.83[CEU][hapmap];0.81[JPT][hapmap];0.91[YRI][hapmap]
rs798512	0.82[CEU][hapmap];0.85[CHB][hapmap];0.93[JPT][hapmap];0.80[ASN][1000 genomes]
rs798513	0.80[ASN][1000 genomes]
rs798518	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs798528	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs798548	0.85[JPT][hapmap]
rs798554	0.85[JPT][hapmap]
rs798557	0.88[CHB][hapmap]
rs960273	1.00[CHB][hapmap];0.93[JPT][hapmap];0.96[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2644274	GNA12	cis	Nerve Tibial	GTEx
rs2644274	GNA12	Cis_1M	lymphoblastoid	RTeQTL
rs2644274	LOC392620	cis	multi-tissue	Pritchard
rs2644274	GNA12	cis	multi-tissue	Pritchard

Chromatin state (count:105 , 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	chr7:2843200-2855200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr7:2843200-2857400	Weak transcription	Brain Germinal Matrix	brain
5	chr7:2843200-2860800	Weak transcription	HSMMtube	muscle
6	chr7:2843200-2864400	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr7:2843400-2854400	Weak transcription	Colonic Mucosa	Colon
8	chr7:2843600-2857200	Weak transcription	Colon Smooth Muscle	Colon
9	chr7:2843600-2860600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr7:2843600-2864400	Weak transcription	Primary T helper cells PMA-I stimulated	--
11	chr7:2843800-2854800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr7:2844000-2858800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr7:2845800-2862200	Weak transcription	K562	blood
14	chr7:2847800-2858800	Weak transcription	HSMM	muscle
15	chr7:2848200-2858800	Weak transcription	NHEK	skin
16	chr7:2848400-2858800	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr7:2848400-2859400	Weak transcription	Fetal Intestine Large	intestine
18	chr7:2848600-2864000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr7:2848800-2854400	Weak transcription	Small Intestine	intestine
20	chr7:2848800-2857200	Weak transcription	Brain Substantia Nigra	brain
21	chr7:2848800-2858400	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr7:2848800-2858600	Weak transcription	Gastric	stomach
23	chr7:2848800-2863400	Weak transcription	Fetal Brain Female	brain
24	chr7:2848800-2874800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr7:2849000-2857200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr7:2849400-2860800	Weak transcription	Stomach Mucosa	stomach
27	chr7:2849600-2866000	Enhancers	Placenta	Placenta
28	chr7:2849800-2855400	Enhancers	NHDF-Ad	bronchial
29	chr7:2851000-2857600	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr7:2851000-2860200	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr7:2851200-2857600	Weak transcription	Fetal Heart	heart
32	chr7:2851200-2858600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr7:2851600-2854400	Weak transcription	Left Ventricle	heart
34	chr7:2851600-2854400	Weak transcription	Pancreas	Pancrea
35	chr7:2851600-2858600	Weak transcription	HMEC	breast
36	chr7:2851600-2858800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr7:2851600-2860600	Weak transcription	Primary B cells from cord blood	blood
38	chr7:2851600-2861000	Weak transcription	Primary hematopoietic stem cells	blood
39	chr7:2851600-2861000	Weak transcription	Brain Cingulate Gyrus	brain
40	chr7:2851600-2869600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr7:2851800-2855000	Enhancers	Right Atrium	heart
42	chr7:2851800-2860400	Weak transcription	Monocytes-CD14+_RO01746	blood
43	chr7:2851800-2882800	Weak transcription	Aorta	Aorta
44	chr7:2852000-2854400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr7:2852000-2854800	Enhancers	HepG2	liver
46	chr7:2852000-2857000	Weak transcription	Liver	Liver
47	chr7:2852000-2857600	Weak transcription	Brain Anterior Caudate	brain
48	chr7:2852000-2858600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr7:2852000-2858800	Weak transcription	Rectal Smooth Muscle	rectum
50	chr7:2852000-2860400	Weak transcription	Brain Hippocampus Middle	brain

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